intro: adapte le projet pour le printemps 2024
- Restructure la feuille de style. - Implémente les adaptation de la feuille de style et du template du projet bunige-template. - Améliore le rendu des exemples de codes. - Complète et adapte les notes du déroulé. - Restructure et complète le contenu de l'introduction pour une présentation d'une demi-heure et pour tenir compte des nouveaux objectifs. - Met à jour les fichiers des références bibliographiques. Co-Authored-by: iGor milhit <igor@milhit.ch>
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tags: [rdv-info, déroulé, markdown]
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---
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## Checklist
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- [ ] Polycopié généré et prêt au partage et ouvert pour s'y référer.
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- [ ] URL du formulaire de feedback prête à être copiée-collée.
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- [ ] Page HackMD ouverte avec un exemple de fichier markdown.
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- [ ] Navigateur de fichier ouvert sur l'ensemble de notes et dans le dossier
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`intro`.
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- [ ] VScode ouvert avec l'ensemble de notes.
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- [ ] Un terminal ouvert dans le dossier `intro` (pour la démo de pandoc).
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## Présentation (2 min.)
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- Présentation.
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@ -15,8 +25,11 @@ tags: [rdv-info, déroulé, markdown]
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- Avantages des fichiers au format texte et de markdown pour la prise de notes.
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- Syntaxe de base.
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- Présentation d'éditeurs.
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- Aperçu des possibilités avancées.
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- Fonctionnalités attendues d'un éditeur.
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- Aperçu des possibilités avancées :
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- Ensemble de notes.
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- Conversion vers d'autres formats (`pandoc`).
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- Insertion d'une référence bibliographique.
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## Présentation
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@ -25,40 +38,62 @@ tags: [rdv-info, déroulé, markdown]
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- Montrer le rendu et la structure.
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- Avantages du format texte :
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- Fichiers simples et légers.
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- Ne dépendant ni d'un logiciel particulier.
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- Ne dépend pas d'un logiciel particulier.
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- Pérennité.
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- Portabilité.
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- Sauvegarde, synchronisation, partage.
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- Recherche textuelle facilitée.
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- Favorise un riche écosystème pour utiliser ou manipuler les fichiers.
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- Inconvénients :
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- Apprentissage simple au début, peut devenir plus ardu selon les besoins.
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- La conversion nécessite l'installation de logiciels supplémentaires.
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- L'usage de `pandoc` pour la conversion se fait dans en « ligne de
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commande ».
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- Le travail collaboratif est possible, mais selon les situations, elle peut
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devenir plus complexe.
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- Conclusion :
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- Rapidité et légèreté adaptée à la prise de note.
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- Notes structurées, recherche textuelle efficace.
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- Adapté pour documents simples (notes) ET pour documents complexes (thèse).
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- Constitution d'une base de connaissance.
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- Détail de la syntaxe depuis HackMD.
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- Importance d'apprendre et d'utiliser régulièrement.
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- Documentation en lien dans le support de cours (page 4).
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- Générateur de tableau en ligne.
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- Intérêt d'apprendre la syntaxe et de l'utiliser régulièrement.
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- Titres.
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- Paragraphes.
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- Italiques et gras.
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- Liens. Sans et avec référence.
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- Image.
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- Éditeurs :
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- Dédiés (typora, abricotine).
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- Bases de connaissance (obsidian).
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- Académique (Zettlr), intégration facilitée de Zotero.
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- Généralistes (visual studio code). Si vous en utiliser déjà un. Si vous
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avez un usage avancé.
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- Fonctionnalités nécessaires :
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- Prévisualisation.
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- Prévisualisation (HackMD).
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- Autocomplétion de la syntaxe.
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- Navigateur de fichiers.
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- Navigateur de fichiers (VScode).
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- Un plus :
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- Correcteur orthographique.
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- Formatage automatique des tableaux.
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- Suivi des liens internes, entre fichiers.
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- Usages avancés :
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- Démo avec Visual Code.
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- Ouvrir README, suivre le lien.
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- Chercher le fichier rdv-info-déroulé.
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- Chercher la chaîne `rdv-info`.
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- Démo avec Visual Code. Ouvrir le dossier `~/bc/`.
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- Ouvrir README, suivre un lien.
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- Chercher un fichier `ctrl+p`.
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- Chercher une chaîne avec `ctrl+shift+f`.
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- Recherche et remplacer une chaîne avec `ctrl+shift+h`.
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- Conversion simple de documents :
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- Aller dans le dossier `~/dev/rdv-info-markdown/intro/`.
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- Afficher le fichier `intro-déroulé.md`.
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- Convertir en DOCX, ODT, PDF et montrer le résultat.
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- Insertion d'une référence bibliographique :
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- Monter que dans le dossier, il y a le fichier `references.bib`.
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- Afficher le contenu du fichier et expliquer brièvement.
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- Monter le *frontmatter* et expliquer.
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- Ajouter le lien vers la bibliographie.
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- Insérer une citation et le titre pour la bibliographie.
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- Convertir en PDF.
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## Après la présentation
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- Partager le lien pour le formulaire de feedback : \
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<https://formulaire.unige.ch/outils/limesurvey3/index.php/664325?&lang=fr>.
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- Mentionner la possibilité d'ateliers pour aller plus loin.
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237
intro/intro.md
237
intro/intro.md
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@ -2,7 +2,7 @@
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title: Introduction à la prise de note avec markdown
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author:
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- Igor Milhit^[Uni CMU]
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date: Printemps 2023
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date: Printemps 2024
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creation_date: 2023-04-19T11:35:14+02:00
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id: 20230419113601
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tags: [note, markdown]
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@ -17,12 +17,13 @@ toc-title: Table des matières
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## Objectifs
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- Quel intérêt ? Pourquoi se mettre à rédiger avec markdown ?
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- Comment : aperçu de la syntaxe de base.
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- Qu'attendre d'un éditeur de texte (pour rédiger avec markdown) ?
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- Avantages et inconvénients.
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- Aperçu de la syntaxe de base.
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- Les fonctionnalités minimales d’un éditeur.
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- Bref aperçu des possibilités avancées :
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- Ensemble de notes.
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- Conversion.
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- Conversion dans d’autres formats.
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- Insertion de références bibliographiques.
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:::{#licence}
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 \
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@ -32,43 +33,46 @@ toc-title: Table des matières
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[cc-by-sa]: https://creativecommons.org/licenses/by-sa/4.0/deed.fr "Texte de la licence en français"
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[sources]: https://git.milhit.ch/igor/rdv-info-markdown
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## Pourquoi ? [^0] {#1st-section}
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## Définition, avantages et inconvénients[^0] {#first-section}
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Le plus important pour *ses* propres habitudes de travail est de trouver des
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méthodes et des outils adaptés à *ses besoins*. Ci-dessous sont listés quelques
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arguments en faveur de l'usage de la syntaxe markdown, mais aucune méthode ou
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Le plus important est de trouver des méthodes et des outils adaptés à *ses
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besoins*. Ci-dessous sont listés quelques arguments en faveur de l'usage de
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fichiers au format texte et de la syntaxe markdown, mais aucune méthode ou
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outil n'est *la* solution miracle pertinente dans *tous* les contextes.
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L'information numérique est utile si elle est **structurée**. Un fichier PDF
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bien conçu donne accès dans la barre latérale à la table des matières pour
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faciliter la navigation. Cette structure s'obtient, par exemple, avec l'usage
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cohérent des styles et des niveaux de titre dans un traitement de texte. La
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syntaxe markdown est une autre méthode, surprenante au début, mais qui s'avère
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particulièrement efficace.[^1]
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### Définition
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Markdown est une syntaxe qui permet, **simplement avec des éléments textuels**,
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de structurer (niveau de titres) et de mettre en forme du texte. Cette
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structure et cette mise en forme sont compréhensibles par des êtres humains et
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par des programmes informatiques. Aussi, les documents rédigés à l'aide de
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markdown peuvent soit être lus tels quels, soit être traités par un
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programme pour afficher un « rendu » sous forme de page web, de document PDF ou
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DOCX.
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L'information numérique est utile si elle est **structurée**. La table des
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matières d'un document numérique devrait être constituée de liens vers les
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sections. Cette structure peut s'obtenir par l'usage des styles et des niveaux
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de titre dans un traitement de texte (Microsoft Word, Libreoffice Writer,
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etc.). La syntaxe markdown est une autre méthode, très efficace.[^1]
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Markdown est *un langage de balisage léger*. Concrètement, il s'agit d'une
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syntaxe qui permet, **uniquement avec des éléments textuels**, de structurer
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(niveau de titres) et de mettre en forme du texte. Cette structure et cette
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mise en forme sont compréhensibles par des êtres humains ou par des programmes
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informatiques. Aussi, les documents rédigés à l'aide de markdown peuvent soit
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être lus tels quels, soit être traités par un programme pour afficher un
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« rendu » sous forme de page web, de document PDF ou DOCX.
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La syntaxe markdown est relativement simple à apprendre et mémoriser. Aussi, la
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rédaction au format markdown repose sur très peu de fonctionnalités du
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logiciel. Le bloc note suffit, même si un peu plus de confort est souhaitable.
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Cette syntaxe est utilisée par de nombreux logiciels ou services en lignes pour
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la rédaction. C'est le cas des notes dans Zotero ou d'éditeurs en ligne
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adaptés au travail collaboratif ([HedgeDoc][hd], [HackMD][hm], etc.).
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la rédaction. C'est le cas des notes dans Zotero ou d'éditeurs en ligne adaptés
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au travail collaboratif ([HedgeDoc][1], [HackMD][2], etc.).
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### Avantages
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Les fichiers utilisés ne sont composés que de caractères textuels. Aussi, ils
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sont :
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- Simples et légers :
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- Ne dépendent pas d'un logiciel spécifique, ni d'un système d'exploitation.
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- Pourront être lus et édités dans n'importe quel contexte, et probablement
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dans un avenir éloigné (pérennité).
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- Pourront être ouverts et édités dans n'importe quel contexte, et
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probablement dans un avenir éloigné (pérennité).
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- Rapides à ouvrir. Avec n'importe quel éditeur de texte (bloc note Windows,
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Notepad++, TextEdit, Gedit, VIM, EMACS, etc.)
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- Faciles à sauvegarder, copier, synchroniser, partager.
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@ -83,43 +87,71 @@ Grâce à ces propriétés, il est possible :
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- De prendre des notes au clavier rapidement, de manière structurée, et avec
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une recherche interne efficace.
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- De rédiger des documents simples ou complexes, petits comme une fiche de
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notes ou volumineux comme une thèse.
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- De rédiger des documents simples (une note) ou complexes (une thèse).
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- De regrouper un ensemble de notes dans un « bloc note » numérique et de
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naviguer rapidement dans cet ensemble, de rechercher de l'information
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facilement.
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naviguer dans cet ensemble, de rechercher de l'information .
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- De manière similaire, de regrouper un ensemble de fichiers pour constituer un
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document complexe, comme un livre ou un article scientifique.
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- Enfin de convertir à partir des même fichiers le document dans plusieurs
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formats pour une diffusion sur le web, la lecture dans un PDF ou un ePub.
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- Enfin de convertir à partir des mêmes fichiers le document dans plusieurs
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formats pour une diffusion sur le web, la lecture dans un PDF ou un ePub
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(compatible avec une liseuse électronique).
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Enfin, il y a deux arguments de *geek* :
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Enfin, les fichiers textuels sont particulièrement adaptés au suivi de
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l'historique des modification (*versioning*), par exemple avec le logiciel
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[Git][3].
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- Les fichiers textuels sont particulièrement adaptés pour en suivre
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l'historique des modification (*versioning*), par exemple avec le logiciel
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[Git][git].
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- Jouer avec markdown et les conversions dans de multiples format est vraiment
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amusant, bien que parfois source de complications inutiles. 😅
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### Inconvénients
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[text]: https://www.arthurperret.fr/cours/format-texte.html
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[hd]: https://hedgedoc.org/
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[hm]: https://hackmd.io/
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[git]: https://fr.wikipedia.org/wiki/Git "Article Wikipedia en français"
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Pour un usage simple, l'apprentissage n'est pas très difficile. La syntaxe de
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base s'acquiert rapidement. Pour parvenir à rédiger des documents relativement
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complexes (notes, citations et bibliographies, etc.), cet apprentissage est un
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peu plus long. Afin de maîtriser la conversion dans différents formats, tout en
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personnalisant la mise en forme des documents obtenus, il devient vite
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nécessaire d'apprendre à utiliser d'autres outils, à modifier des modèles dans
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les formats désirés (HTML, DOCX, peut-être LaTeX, etc.).
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## Comment ?
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Certains éditeurs intègrent la fonction de conversion, mais elle repose sur
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l'installation de logiciels annexes, principalement `pandoc`, mais aussi une
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distribution LaTeX pour obtenir une conversion en PDF. Ces outils ne sont pas
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si difficiles à installer. Surtout, ils sont libres, gratuits et disponibles
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pour Windows, Mac OS ou Linux.
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La syntaxe markdown est très souvent expliquée sur le web :
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Pour utiliser `pandoc`, qui est l'outil de conversion le plus complet, il est
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nécessaire de le faire « en ligne de commande » plutôt que dans une interface
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graphique, avec la souris. C'est un élément en plus à apprendre, mais qui ouvre
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beaucoup de possibilités.
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Le travail collaboratif à plusieurs est toujours possible, mais selon les cas
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avec une certaine friction. La situation la plus simple est d'utiliser un
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éditeur en ligne qui offre des fonctionnalités d'édition à plusieurs. Souvent
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cela est au prix de ne pouvoir disposer de toute la puissance de `pandoc`, du
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moins directement.
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Toujours dans le cas où toutes les personnes qui collaborent sont capables de
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travailler avec les mêmes outils, elles peuvent toujours travailler ensemble en
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se mettant d'accord sur un « workflow », par exemple grâce à `git` mentionné
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plus haut. Mais c'est un outil de plus à apprendre. Et de nouvelles
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possibilités à découvrir.
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Enfin, si les personnes avec qui on collabore ne veulent ou ne peuvent pas
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utiliser les mêmes méthodes, alors il faudra mettre en place un processus
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d'export et d'import un peu complexe, mais en partie automatisable
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[@perretMarkdownTraitementTexte2022].
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## La syntaxe markdown
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La syntaxe markdown est très bien documentée sur le web :
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- La documentation « officielle » est disponible sur le site personnel d'un des
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concepteurs de la syntaxe : <https://daringfireball.net/projects/markdown/>
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[@gruberMarkdown2004].
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- Le site *flus* propose Une documentation en français et très claire :
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<https://flus.fr/carnet/markdown.html> [@fressinaudGuideMarkdown2022].
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- Il y a plusieurs variantes de la syntaxe et un site essaie de proposer un
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standard. Il met à disposition un tutoriel interactif :
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- Il y a plusieurs variantes (ou extensions) de la syntaxe et un site essaie de
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proposer un standard. Il met à disposition un tutoriel interactif :
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<https://commonmark.org/help/> [@commonmarkCommonMark].
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- Arthur Perret a traduit en français ce même tutoriel, disponible sur sa page
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qui explique ce qu'est markdown :
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expliquant ce qu'est markdown :
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<https://www.arthurperret.fr/cours/markdown.html> [@perretMarkdown2022].
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Pour les tableaux, il est fortement conseillé :
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@ -144,13 +176,16 @@ en deux grandes catégories :
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Dans les deux cas, des fonctionnalités de base qui sont presque
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incontournables :
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|
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- Une prévisualisation, le plus souvent sour la forme d'un *rendu* HTML.
|
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- La possibilité de naviguer dans une arborescence de fichiers.
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- Une prévisualisation, le plus souvent sous la forme d'un *rendu* HTML. Cette
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fonctionnalité a l'avantage de permettre de se faire une idée du résultat
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sans devoir générer le fichier final.
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- La possibilité de naviguer dans une arborescence de fichiers, en général dans
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une barre sur le côté de l'interface.
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- Une autocomplétion, pour faciliter l'entrée de syntaxe avec des `[]` ou des
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`()`.
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D'autres fonctionnalités ne sont pas indispensables, mais deviennent rapidement
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assez utiles :
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utiles :
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- La correction orthographique pour les langues dans lesquelles vous rédigez.
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- Un formatage automatique des tableaux.
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@ -166,7 +201,7 @@ votre appareil (ordinateur, tablette, téléphone) ou d'un service web.
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**Typora** est éditeur qui met l'accent sur son interface épurée. Il est disponible
|
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pour tous les systèmes d'exploitation, payant. <https://typora.io/>
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|
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![Interface de GhostWriter][gw]
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![Interface de GhostWriter][6]
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|
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**GhostWriter** est libre et gratuit, pour Windows et Linux
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principalement.[^2] <https://ghostwriter.kde.org/fr/>
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|
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@ -183,29 +218,26 @@ se limite pas à l'édition de fichiers markdown, mais permet de constituer une
|
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base de connaissance basée sur des notes, et cela de manière très complète.
|
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<https://obsidian.md/>
|
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|
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![Interface de Zettlr][zettlr]
|
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![Interface de Zettlr][5]
|
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|
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**Zettlr** est libre et disponible pour tous les systèmes d'exploitation. Il
|
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est destiné à un usage académique, que ce soit pour construire une base de
|
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connaissance à partir de notes ou pour rédiger un travail de mémoire ou un
|
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article scientifique. Il intègre Zotero pour la gestion des références.
|
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|
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En ligne, on peut mentionner à nouveau le service [HackMD][hm] ou le logiciel
|
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[HedgeDoc][hd] qui permet non seulement d'éditer des fichiers mardkown avec une
|
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En ligne, on peut mentionner à nouveau le service [HackMD][2] ou le logiciel
|
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[HedgeDoc][1] qui permet non seulement d'éditer des fichiers markdown avec une
|
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prévisualisation, mais également de le faire à plusieurs, de disposer d'un
|
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suivi des modfications et de commenter.
|
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suivi des modifications et de commenter.
|
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|
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![Interface de l'éditeur HackMD][interface-hd]
|
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![Interface de l'éditeur HackMD][4]
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[interface-hd]: ../static/hackmd.png
|
||||
[zettlr]: ../static/zettlr.png
|
||||
[gw]: ../static/ghostwriter.png
|
||||
|
||||
### Éditeurs généralistes
|
||||
|
||||
*Généralistes* car ces éditeurs ne sont pas limités à l'édition de fichier
|
||||
markdown. Le plus souvent, ce sont des *éditeurs de texte*, en général utilisés
|
||||
par des développeurs pour écrire du code informatique. Normalement, ils
|
||||
markdown. Le plus souvent, ce sont des *éditeurs de texte* utilisés
|
||||
par des développeurs pour écrire du code informatique. Le plus souvent, ils
|
||||
disposent d'un écosystème d'extensions afin de s'adapter à des besoins
|
||||
spécifiques. De ce fait, ils sont très puissants.
|
||||
|
||||
|
|
@ -218,9 +250,7 @@ suivant, notamment :
|
|||
- VIM ou neovim, libre et gratuit, pour tous les systèmes d'exploitation.
|
||||
- EMACS, libre et gratuit.
|
||||
|
||||
![Interface de Visual Studio Code][vscode]
|
||||
|
||||
[vscode]: ../static/vscode.png
|
||||
![Interface de Visual Studio Code][7]
|
||||
|
||||
## Aperçu des possibilités avancées
|
||||
|
||||
|
|
@ -231,10 +261,10 @@ dans le même répertoires (y compris avec des sous répertoires) et de faire de
|
|||
liens entre les fichiers (et même au sein d'un seul fichier).
|
||||
|
||||
Certains éditeurs, ou certaines extensions d'éditeurs, proposent des facilités
|
||||
pour générer ces liens, au prix d'une syntaxe *ad hoc*. Mais il est
|
||||
parfaitement possible de le faire avec la syntaxe « normale » du lien.
|
||||
pour générer ces liens, au prix d'une syntaxe *ad hoc* (« wiki links »). Mais
|
||||
il est parfaitement possible de le faire avec la syntaxe « normale » du lien.
|
||||
|
||||
![Lien depuis le fichier `README.md` vers le fichier `points-a-ameliorer.md`][lienEntreFichiers]
|
||||
![Lien depuis le fichier `README.md` vers le fichier `points-a-ameliorer.md`][8]
|
||||
|
||||
La figure 5 montre sur la gauche une arborescence de fichiers, avec
|
||||
des sous-répertoires, et dans le fichier affiché (`README.md`), un lien vers le
|
||||
|
|
@ -247,7 +277,7 @@ Code. Il y a 13 occurrences du terme dans 7 fichiers. Ce type de recherche est
|
|||
facilité par le fait que ce sont des fichiers au format texte et se retrouve
|
||||
dans la plupart des éditeurs généralistes de qualité.
|
||||
|
||||
![Recherche dans Visual Studio Code][rechCode]
|
||||
![Recherche dans Visual Studio Code][9]
|
||||
|
||||
### Export vers d'autres formats
|
||||
|
||||
|
|
@ -262,16 +292,77 @@ parfois à l'aide de logiciels spécifiques. Par exemple, pour produire un
|
|||
fichier PDF, il peut utiliser plusieurs méthodes, dont LaTeX, ce qui suppose
|
||||
d'en avoir une version installée.
|
||||
|
||||
La commande pour une conversion simple est de la forme suivante :
|
||||
|
||||
```bash
|
||||
pandoc --output fichier.docx fichier.md
|
||||
```
|
||||
|
||||
Le format obtenu correspond à celui qui est indiqué en extension du nom de
|
||||
fichier de sortie `--output`, ici du DOCX. Mais il est possible de
|
||||
l'expliciter :
|
||||
|
||||
```bash
|
||||
pandoc --to docx --output fichier.docx fichier.md
|
||||
```
|
||||
|
||||
Le support de cours de cette introduction à markdown a été rédigée en markdown
|
||||
et est exportée en PDF grâce à `pandoc` et à *Paged.js*.[^3]
|
||||
|
||||
[lienEntreFichiers]: ../static/lien-entre-fichiers.png
|
||||
[rechCode]: ../static/recherche-vscode.png
|
||||
### Citations et Bibliographie
|
||||
|
||||
## Bibliographie
|
||||
Pour insérer des citations et générer une bibliographie, il est nécessaire
|
||||
d'avoir au moins une collection de références bibliographiques, par exemple
|
||||
sous la forme d'un fichier `.bib`. Pour obtenir ce fichier, il est possible de
|
||||
passer par Zotero et d'exporter une collection dans le format BibTex (ou Better
|
||||
BibTex avec l'extension Zotero du même nom.)
|
||||
|
||||
[^0]: Cette section repose beaucoup sur la page [Format texte][text]
|
||||
d'Arthur Perret [@perretFormatTexte2022].
|
||||
Dans ce fichier (et dans Zotero), on trouve pour chaque référence une « clé de
|
||||
citation » qui permet de l'identifier de manière unique. C'est cette clé que
|
||||
l'on va insérer dans notre fichier markdown pour indiquer une citation. Elle
|
||||
est insérée avec la syntaxe suivante : `[@clé-de-citation]`.
|
||||
|
||||
On peut encore ajouter à la fin de notre fichier un titre de deuxième niveau
|
||||
avec le texte bibliographie, pour que `pandoc` puisse y insérer la
|
||||
bibliographie.
|
||||
|
||||
Pour être en mesure de traiter ces informations, il faut utiliser l'option de
|
||||
`--citeproc` intégrée dans `pandoc` :
|
||||
|
||||
```bash
|
||||
pandoc --citeproc \
|
||||
--to=pdf --pdf-engine=xelatex \
|
||||
--bibliography=references.bib \
|
||||
--output fichier.pdf fichier.md
|
||||
```
|
||||
|
||||
Dans l'exemple ci-dessus, nous voyons l'option `--citeproc` et l'option
|
||||
`--bibliography=` qui indique où se trouve le fichier des références
|
||||
bibliographiques. Par défaut le style est Chicago, de type auteur-date.
|
||||
|
||||
Pour aller plus loin, le mieux est de consulter la [documentation
|
||||
officielle][10] de `pandoc.`
|
||||
|
||||
## Bibliographie {#bibliography}
|
||||
|
||||
<!-- liens -->
|
||||
|
||||
[0]: https://www.arthurperret.fr/cours/format-texte.html
|
||||
[1]: https://hedgedoc.org/
|
||||
[2]: https://hackmd.io/
|
||||
[3]: https://fr.wikipedia.org/wiki/Git "Article Wikipedia en français"
|
||||
[4]: ../static/hackmd.png
|
||||
[5]: ../static/zettlr.png
|
||||
[6]: ../static/ghostwriter.png
|
||||
[7]: ../static/vscode.png
|
||||
[8]: ../static/lien-entre-fichiers.png
|
||||
[9]: ../static/recherche-vscode.png
|
||||
[10]: https://pandoc.org/MANUAL.html#citations
|
||||
|
||||
<!-- notes -->
|
||||
|
||||
[^0]: Cette section repose beaucoup sur la page [Format texte][0] d'Arthur
|
||||
Perret [@perretFormatTexte2022].
|
||||
[^1]: Markdown n'est pas le seul langage de balisage léger existant, bien que
|
||||
ce soit le plus répandu. D'autres sont encore plus robustes ou puissants, comme
|
||||
*RestructuredText* ou *AsciiDoc*.
|
||||
|
|
|
|||
|
|
@ -0,0 +1,370 @@
|
|||
@article{bunchIndirectReferenceIntervals2022,
|
||||
title = {Indirect Reference Intervals Using an {{R}} Pipeline.},
|
||||
author = {Bunch, Dustin R.},
|
||||
date = {2022-04},
|
||||
journaltitle = {J Mass Spectrom Adv Clin Lab},
|
||||
volume = {24},
|
||||
eprint = {35252947},
|
||||
eprinttype = {pmid},
|
||||
pages = {22--30},
|
||||
location = {Netherlands},
|
||||
issn = {2667-145X 2667-1468},
|
||||
doi = {10.1016/j.jmsacl.2022.02.004},
|
||||
abstract = {BACKGROUND: Indirect reference intervals require robust statistical approaches to separate the pathological and healthy values. This can be achieved with a data pipeline created in R, a freely available statistical programming language. METHODS: A data pipeline was created to ingest, partition, normalize, remove outliers, and identify reference intervals for testosterone (Testo; n ~=~7,207) and aspartate aminotransferase (AST; n ~=~5,882) using data sets from NHANES. RESULTS: The estimates for AST and Testo determined by this pipeline approximated current RIs. Care should be taken when using this pipeline as there are limitations that depend on the pathology of the analyte and the data set being used for RI estimation. CONCLUSIONS: R can be used to create a robust statistical reference interval pipeline.},
|
||||
langid = {english},
|
||||
pmcid = {PMC8889237},
|
||||
keywords = {ANOVA Analysis of variance,AST aspartate aminotransferase,CLSI Clinical Laboratory Standards Institute,cmu,EHR electronic health record,IFCC International Federation of Clinical Chemistry and Laboratory Medicine,LC-MS/MS Liquid chromatography tandem mass spectrometry,LIS Laboratory informatics system,markdown,Mixtools,non lu,pubmed,R markdown,R markdown tutorial,Reference interval,RI reference interval,SDI Standard deviation index,SDR Standard deviation ratio,Testo Testosterone,TukeyHSD Tukey multiple pairwise-comparisons,z5 Critical z-score},
|
||||
file = {/home/igor/Zotero/storage/YYP9JQTY/Bunch_2022_Indirect reference intervals using an R pipeline.pdf}
|
||||
}
|
||||
|
||||
@article{chapmanExpectedPosterioriScoring2022,
|
||||
title = {Expected a Posteriori Scoring in {{PROMIS}}(®).},
|
||||
author = {Chapman, Robert},
|
||||
date = {2022-06-03},
|
||||
journaltitle = {J Patient Rep Outcomes},
|
||||
volume = {6},
|
||||
number = {1},
|
||||
eprint = {35657454},
|
||||
eprinttype = {pmid},
|
||||
pages = {59},
|
||||
location = {Germany},
|
||||
issn = {2509-8020},
|
||||
doi = {10.1186/s41687-022-00464-9},
|
||||
abstract = {BACKGROUND: The Patient-Reported Outcome Measurement Information System(®) (PROMIS(®)) was developed to reliably measure health-related quality of life using the patient's voice. To achieve these aims, PROMIS utilized Item Response Theory methods in its development, validation and implementation. PROMIS measures are typically scored using a specific method to calculate scores, called Expected A Posteriori estimation. BODY: Expected A Posteriori scoring methods are flexible, produce accurate scores and can be efficiently calculated by statistical software. This work seeks to make Expected A Posteriori scoring methods transparent and accessible to a larger audience through description, graphical demonstration and examples. Further applications and practical considerations of Expected A Posteriori scoring are presented and discussed. All materials used in this paper are made available through the R Markdown reproducibility framework and are intended to be reviewed and reused. Commented statistical code for the calculation of Expected A Posteriori scores is included. CONCLUSION: This work seeks to provide the reader with a summary and visualization of the operation of Expected A Posteriori scoring, as implemented in PROMIS. As PROMIS is increasingly adopted and implemented, this work will provide a basis for making psychometric methods more accessible to the PROMIS user base.},
|
||||
langid = {english},
|
||||
pmcid = {PMC9166925},
|
||||
keywords = {cmu,markdown,non lu,pubmed,R markdown},
|
||||
file = {/home/igor/Zotero/storage/7R2KLGBS/Chapman_2022_Expected a posteriori scoring in PROMIS(®).pdf}
|
||||
}
|
||||
|
||||
@online{commonmarkCommonMark,
|
||||
title = {{{CommonMark}}},
|
||||
author = {CommonMark},
|
||||
url = {https://commonmark.org/},
|
||||
urldate = {2023-04-25},
|
||||
langid = {english},
|
||||
organization = {CommonMark},
|
||||
keywords = {cmu,non lu},
|
||||
file = {/home/igor/Zotero/storage/ESNTHT9H/commonmark.org.html}
|
||||
}
|
||||
|
||||
@article{considineToolEncourageMinimum2019,
|
||||
title = {A {{Tool}} to {{Encourage Minimum Reporting Guideline Uptake}} for {{Data Analysis}} in {{Metabolomics}}.},
|
||||
author = {Considine, Elizabeth C. and Salek, Reza M.},
|
||||
date = {2019-03-05},
|
||||
journaltitle = {Metabolites},
|
||||
volume = {9},
|
||||
number = {3},
|
||||
eprint = {30841575},
|
||||
eprinttype = {pmid},
|
||||
location = {Switzerland},
|
||||
issn = {2218-1989},
|
||||
doi = {10.3390/metabo9030043},
|
||||
abstract = {Despite the proposal of minimum reporting guidelines for metabolomics over a decade ago, reporting on the data analysis step in metabolomics studies has been shown to be unclear and incomplete. Major omissions and a lack of logical flow render the data analysis' sections in metabolomics studies impossible to follow, and therefore replicate or even imitate. Here, we propose possible reasons why the original reporting guidelines have had poor adherence and present an approach to improve their uptake. We present in this paper an R markdown reporting template file that guides the production of text and generates workflow diagrams based on user input. This R Markdown template contains, as an example in this instance, a set of minimum information requirements specifically for the data pre-treatment and data analysis section of biomarker discovery metabolomics studies, (gleaned directly from the original proposed guidelines by Goodacre at al). These minimum requirements are presented in the format of a questionnaire checklist in an R markdown template file. The R Markdown reporting template proposed here can be presented as a starting point to encourage the data analysis section of a metabolomics manuscript to have a more logical presentation and to contain enough information to be understandable and reusable. The idea is that these guidelines would be open to user feedback, modification and updating by the metabolomics community via GitHub.},
|
||||
langid = {english},
|
||||
pmcid = {PMC6468746},
|
||||
keywords = {cmu,data analysis,markdown,minimum guidelines,non lu,pubmed,R markdown,reporting,reproducibility},
|
||||
file = {/home/igor/Zotero/storage/RSRUDDYS/Considine_Salek_2019_A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in.pdf}
|
||||
}
|
||||
|
||||
@article{daasDynamicPublicationMedia2022,
|
||||
title = {Dynamic Publication Media with the {{COPASI R Connector}} ({{CoRC}}).},
|
||||
author = {Daas, Johanna C. J. and Förster, Jonas D. and Pahle, Jürgen},
|
||||
date = {2022-06},
|
||||
journaltitle = {Math Biosci},
|
||||
volume = {348},
|
||||
eprint = {35452633},
|
||||
eprinttype = {pmid},
|
||||
pages = {108822},
|
||||
location = {United States},
|
||||
issn = {1879-3134 0025-5564},
|
||||
doi = {10.1016/j.mbs.2022.108822},
|
||||
abstract = {In this article we show how dynamic publication media and the COPASI R Connector (CoRC) can be combined in a natural and synergistic way to communicate (biochemical) models. Dynamic publication media are becoming a popular tool for authors to effectively compose and publish their work. They are built from templates and the final documents are created dynamically. In addition, they can also be interactive. Working with dynamic publication media is made easy with the programming environment R via its integration with tools such as R Markdown, Jupyter and Shiny. Additionally, the COmplex PAthway SImulator COPASI (http://www.copasi.org), a widely used biochemical modelling toolkit, is available in R through the use of the COPASI R Connector (CoRC, https://jpahle.github.io/CoRC). Models are a common tool in the mathematical biosciences, in particular kinetic models of biochemical networks in (computational) systems biology. We focus on three application areas of dynamic publication media and CoRC: Documentation (reproducible workflows), Teaching (creating self-paced lessons) and Science Communication (immersive and engaging presentation). To illustrate these, we created six dynamic document examples in the form of R Markdown and Jupyter notebooks, hosted on the platforms GitHub, shinyapps.io, Google Colaboratory. Having code and output in one place, creating documents in template-form and the option of interactivity make the combination of dynamic documents and CoRC a versatile tool. All our example documents are freely available at https://jpahle.github.io/DynamiCoRC under the Creative Commons BY 4.0 licence.},
|
||||
langid = {english},
|
||||
keywords = {*Software,*Systems Biology,cmu,COPASI,CoRC,Dynamic publication media,Jupyter,Kinetics,markdown,non lu,pubmed,R markdown,Systems biology},
|
||||
file = {/home/igor/Zotero/storage/WJ5FCFZY/Daas et al_2022_Dynamic publication media with the COPASI R Connector (CoRC).pdf}
|
||||
}
|
||||
|
||||
@unpublished{deletrazModeTexteMarkdown2022,
|
||||
type = {Atelier},
|
||||
title = {En mode texte\,: Markdown, Stylo, Pandoc, Notebook…},
|
||||
author = {Deletraz, Gaëlle and Rabaud, Julien},
|
||||
date = {2022},
|
||||
url = {https://markdown-somate2022.netlify.app},
|
||||
urldate = {2023-04-17},
|
||||
eventtitle = {So-Mate 2022},
|
||||
langid = {fre},
|
||||
venue = {Pau},
|
||||
keywords = {cmu,markdown,non lu,pandoc,Publication scientifique}
|
||||
}
|
||||
|
||||
@online{eyssetteUtiliserMarkdownPour2023,
|
||||
type = {Mastodon post},
|
||||
title = {Utiliser le Markdown pour tout faire.Le diaporama (fait en markdown bien sûr !) qui m'a servi de support lors de mon atelier pour la Journée…},
|
||||
author = {Eyssette, Cédric (@eyssette@scholar.social)},
|
||||
date = {2023-04-07},
|
||||
url = {https://scholar.social/@eyssette/110158455766516456},
|
||||
urldate = {2023-04-17},
|
||||
abstract = {Utiliser le Markdown pour tout faire.Le diaporama (fait en markdown bien sûr !) qui m'a servi de support lors de mon atelier pour la Journée du Libre Éducatif 2023.https://eyssette.forge.aeif.fr/marp-slides/slides/2022-2023/utiliser-le-markdown-pour-tout-faire\#Markdown\#JDLE\#JDLE2023\#TeamEduc\#MastoProf},
|
||||
langid = {french},
|
||||
organization = {Mastodon},
|
||||
keywords = {cmu,fediverse,markdown,mastodon,non lu},
|
||||
file = {/home/igor/Zotero/storage/7FYFNED6/110158455766516456.html}
|
||||
}
|
||||
|
||||
@unpublished{eyssetteUtiliserMarkdownPour2023a,
|
||||
title = {Utiliser le markdown pour tout faire},
|
||||
author = {Eyssette, Cédric},
|
||||
date = {2023},
|
||||
url = {https://eyssette.forge.aeif.fr/marp-slides/slides/2022-2023/utiliser-le-markdown-pour-tout-faire},
|
||||
urldate = {2023-04-17},
|
||||
langid = {fre},
|
||||
keywords = {cmu,non lu},
|
||||
file = {/home/igor/Zotero/storage/I7CTE3X5/utiliser-le-markdown-pour-tout-faire.html}
|
||||
}
|
||||
|
||||
@online{fressinaudGuideMarkdown2022,
|
||||
type = {Site d'une application web},
|
||||
title = {Guide Markdown},
|
||||
author = {Fressinaud, Marien},
|
||||
date = {2022-07-11},
|
||||
url = {https://flus.fr/carnet/markdown.html},
|
||||
urldate = {2023-04-17},
|
||||
abstract = {Un guide simple pour apprendre Markdown.},
|
||||
langid = {fre},
|
||||
organization = {flus},
|
||||
keywords = {cmu,documentation,markdown,non lu},
|
||||
file = {/home/igor/Zotero/storage/96VGWVYV/markdown.html}
|
||||
}
|
||||
|
||||
@article{graysonMarkdownDynamicInterface2022,
|
||||
title = {R {{Markdown}} as a Dynamic Interface for Teaching: {{Modules}} from Math and Biology Classrooms.},
|
||||
author = {Grayson, Kristine L. and Hilliker, Angela K. and Wares, Joanna R.},
|
||||
date = {2022-07},
|
||||
journaltitle = {Math Biosci},
|
||||
volume = {349},
|
||||
eprint = {35623397},
|
||||
eprinttype = {pmid},
|
||||
pages = {108844},
|
||||
location = {United States},
|
||||
issn = {1879-3134 0025-5564},
|
||||
doi = {10.1016/j.mbs.2022.108844},
|
||||
abstract = {Advancing technologies, including interactive tools, are changing classroom pedagogy across academia. Here, we discuss the R Markdown interface, which allows for the creation of partial or complete interactive classroom modules for courses using the R programming language. R Markdown files mix sections of R code with formatted text, including LaTeX, which are rendered together to form complete reports and documents. These features allow instructors to create classroom modules that guide students through concepts, while providing areas for coding and text response by students. Students can also learn to create their own reports for more independent assignments. After presenting the features and uses of R Markdown to enhance teaching and learning, we present examples of materials from two courses. In a Computational Modeling course for math students, we used R Markdown to guide students through exploring mathematical models to understand the principle of herd immunity. In a Data Visualization and Communication course for biology students, we used R Markdown for teaching the fundamentals of R programming and graphing, and for students to learn to create reproducible data investigations. Through these examples, we demonstrate the benefits of R Markdown as a dynamic teaching and learning tool.},
|
||||
langid = {english},
|
||||
pmcid = {PMC9487201},
|
||||
keywords = {*Learning,*Students,Biology/education,cmu,Data visualization,Herd immunity,Humans,markdown,non lu,Pedagogy,pubmed,R markdown,Teaching programming},
|
||||
file = {/home/igor/Zotero/storage/JQGHBHB5/Grayson et al_2022_R Markdown as a dynamic interface for teaching.pdf}
|
||||
}
|
||||
|
||||
@online{gruberMarkdown2004,
|
||||
type = {Site personnel},
|
||||
title = {Markdown},
|
||||
author = {Gruber, John},
|
||||
date = {2004-12-17},
|
||||
url = {https://daringfireball.net/projects/markdown/},
|
||||
urldate = {2023-04-17},
|
||||
langid = {english},
|
||||
organization = {Daring Fireball},
|
||||
keywords = {cmu,documentation,markdown,non lu},
|
||||
file = {/home/igor/Zotero/storage/J7WP5B3D/markdown.html}
|
||||
}
|
||||
|
||||
@article{hershbergJBrowseRInterfaceJBrowse2021,
|
||||
title = {{{JBrowseR}}: An {{R}} Interface to the {{JBrowse}} 2 Genome Browser.},
|
||||
author = {Hershberg, Elliot A. and Stevens, Garrett and Diesh, Colin and Xie, Peter and De Jesus Martinez, Teresa and Buels, Robert and Stein, Lincoln and Holmes, Ian},
|
||||
date = {2021-11-05},
|
||||
journaltitle = {Bioinformatics},
|
||||
volume = {37},
|
||||
number = {21},
|
||||
eprint = {34196689},
|
||||
eprinttype = {pmid},
|
||||
pages = {3914--3915},
|
||||
location = {England},
|
||||
issn = {1367-4811 1367-4803},
|
||||
doi = {10.1093/bioinformatics/btab459},
|
||||
abstract = {MOTIVATION: Genome browsers are an essential tool in genome analysis. Modern genome browsers enable complex and interactive visualization of a wide variety of genomic data modalities. While such browsers are very powerful, they can be challenging to configure and program for bioinformaticians lacking expertise in web development. RESULTS: We have developed an R package that provides an interface to the JBrowse 2 genome browser. The package can be used to configure and customize the browser entirely with R code. The browser can be deployed from the R console, or embedded in Shiny applications or R Markdown documents. AVAILABILITY AND IMPLEMENTATION: JBrowseR is available for download from CRAN, and the source code is openly available from the Github repository at https://github.com/GMOD/JBrowseR/.},
|
||||
langid = {english},
|
||||
pmcid = {PMC8570803},
|
||||
keywords = {*Genome,*Genomics,cmu,markdown,non lu,pubmed,R markdown,Software},
|
||||
file = {/home/igor/Zotero/storage/LYEIF748/Hershberg et al_2021_JBrowseR.pdf}
|
||||
}
|
||||
|
||||
@article{jaglaSCHNAPPsSingleCell2021,
|
||||
title = {{{SCHNAPPs}} - {{Single Cell sHiNy APPlication}}(s).},
|
||||
author = {Jagla, Bernd and Libri, Valentina and Chica, Claudia and Rouilly, Vincent and Mella, Sebastien and Puceat, Michel and Hasan, Milena},
|
||||
date = {2021-12},
|
||||
journaltitle = {J Immunol Methods},
|
||||
volume = {499},
|
||||
eprint = {34742775},
|
||||
eprinttype = {pmid},
|
||||
pages = {113176},
|
||||
location = {Netherlands},
|
||||
issn = {1872-7905 0022-1759},
|
||||
doi = {10.1016/j.jim.2021.113176},
|
||||
abstract = {Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed to guide the investigation. Thus, there is an increasing need to develop applications geared towards bench-scientists to help them abstract the technical challenges of the analysis so that they can focus on the science at play. It is also expected that such applications should support closer collaboration between bioinformaticians and bench-scientists by providing reproducible science tools. We present SCHNAPPs, a Graphical User Interface (GUI), designed to enable bench-scientists to autonomously explore and interpret scRNAseq data and associated annotations. The R/Shiny-based application allows following different steps of scRNAseq analysis workflows from Seurat or Scran packages: performing quality control on cells and genes, normalizing the expression matrix, integrating different samples, dimension reduction, clustering, and differential gene expression analysis. Visualization tools for exploring each step of the process include violin plots, 2D projections, Box-plots, alluvial plots, and histograms. An R-markdown report can be generated that tracks modifications and selected visualizations. The modular design of the tool allows it to easily integrate new visualizations and analyses by bioinformaticians. We illustrate the main features of the tool by applying it to the characterization of T cells in a scRNAseq and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) experiment of two healthy individuals.},
|
||||
langid = {english},
|
||||
keywords = {*Sequence Analysis RNA,*Single-Cell Analysis,*Software,CITE-Seq,cmu,Humans,Leukocytes Mononuclear/*cytology/immunology,markdown,multi-omics data analysis,non lu,pubmed,R markdown,scRNA-seq,Shiny application},
|
||||
file = {/home/igor/Zotero/storage/PEARJ76P/Jagla et al_2021_SCHNAPPs - Single Cell sHiNy APPlication(s).pdf}
|
||||
}
|
||||
|
||||
@article{kariyawasamDashboardstyleInteractivePlots2021,
|
||||
title = {Dashboard-Style Interactive Plots for {{RNA-seq}} Analysis Are {{R Markdown}} Ready with {{Glimma}} 2.0.},
|
||||
author = {Kariyawasam, Hasaru and Su, Shian and Voogd, Oliver and Ritchie, Matthew E. and Law, Charity W.},
|
||||
date = {2021-12},
|
||||
journaltitle = {NAR Genom Bioinform},
|
||||
volume = {3},
|
||||
number = {4},
|
||||
eprint = {34988439},
|
||||
eprinttype = {pmid},
|
||||
pages = {lqab116},
|
||||
location = {England},
|
||||
issn = {2631-9268},
|
||||
doi = {10.1093/nargab/lqab116},
|
||||
abstract = {Glimma 1.0 introduced intuitive, point-and-click interactive graphics for differential gene expression analysis. Here, we present a major update to Glimma that brings improved interactivity and reproducibility using high-level visualization frameworks for R and JavaScript. Glimma 2.0 plots are now readily embeddable in R Markdown, thus allowing users to create reproducible reports containing interactive graphics. The revamped multidimensional scaling plot features dashboard-style controls allowing the user to dynamically change the colour, shape and size of sample points according to different experimental conditions. Interactivity was enhanced in the MA-style plot for comparing differences to average expression, which now supports selecting multiple genes, export options to PNG, SVG or CSV formats and includes a new volcano plot function. Feature-rich and user-friendly, Glimma makes exploring data for gene expression analysis more accessible and intuitive and is available on Bioconductor and GitHub.},
|
||||
langid = {english},
|
||||
pmcid = {PMC8693569},
|
||||
keywords = {cmu,markdown,non lu,pubmed,R markdown},
|
||||
file = {/home/igor/Zotero/storage/ZQD2WXNN/Kariyawasam et al_2021_Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready.pdf}
|
||||
}
|
||||
|
||||
@online{masuttiRedigerManipulerDocuments2019,
|
||||
title = {Rédiger et manipuler des documents avec Markdown},
|
||||
author = {Masutti, Christophe},
|
||||
date = {2019-05-08},
|
||||
url = {https://golb.statium.link/post/20190528rediger-et-manipuler-des-documents-markdown/},
|
||||
urldate = {2024-03-19},
|
||||
langid = {fre},
|
||||
organization = {Statium : blog},
|
||||
keywords = {cmu,markdown,non lu,pandoc,publication numérique,Publication scientifique}
|
||||
}
|
||||
|
||||
@article{ovadiaMarkdownLibrariansAcademics2014a,
|
||||
title = {Markdown for {{Librarians}} and {{Academics}}},
|
||||
author = {Ovadia, Steven},
|
||||
date = {2014-04-03},
|
||||
journaltitle = {Behavioral \& Social Sciences Librarian},
|
||||
volume = {33},
|
||||
number = {2},
|
||||
pages = {120--124},
|
||||
issn = {0163-9269, 1544-4546},
|
||||
doi = {10.1080/01639269.2014.904696},
|
||||
url = {http://www.tandfonline.com/doi/abs/10.1080/01639269.2014.904696},
|
||||
urldate = {2023-05-02},
|
||||
langid = {english},
|
||||
keywords = {cmu,markdown,non lu,Publication scientifique},
|
||||
file = {/home/igor/Zotero/storage/25MP4P3N/Ovadia_2014_Markdown for Librarians and Academics.pdf}
|
||||
}
|
||||
|
||||
@online{paged.jsPagedJs,
|
||||
title = {About {{Paged}}.Js?},
|
||||
author = {Paged.js},
|
||||
url = {https://pagedjs.org/about/},
|
||||
urldate = {2024-03-08},
|
||||
langid = {english},
|
||||
organization = {Paged.js},
|
||||
keywords = {édition numérique,non lu,publication numérique}
|
||||
}
|
||||
|
||||
@online{pandocWritingThesisThinking2023,
|
||||
type = {Mastodon post},
|
||||
title = {Writing a \#thesis? {{Thinking}} about Doing It in \#{{Markdown}}? {{No}} Problem, {{Tom Pollard}} Has You Covered.{{https://github.com/tompollard/phd\_thesis\_ma…}}},
|
||||
shorttitle = {Writing a \#thesis?},
|
||||
author = {{pandoc}, (@pandoc@fosstodon.org)},
|
||||
date = {2023-04-12},
|
||||
url = {https://fosstodon.org/@pandoc/110184589069297715},
|
||||
urldate = {2023-04-17},
|
||||
abstract = {Writing a \#thesis? Thinking about doing it in \#Markdown? No problem, Tom Pollard has you covered.https://github.com/tompollard/phd\_thesis\_markdown},
|
||||
langid = {english},
|
||||
organization = {Mastodon},
|
||||
keywords = {cmu,fediverse,markdown,mastodon,non lu,pandoc,Publication scientifique},
|
||||
file = {/home/igor/Zotero/storage/T354LYSW/110184589069297715.html}
|
||||
}
|
||||
|
||||
@article{perretFormatTexte2022,
|
||||
title = {Format texte},
|
||||
author = {Perret, Arthur},
|
||||
date = {2022-12-11},
|
||||
journaltitle = {Arthur Perret},
|
||||
url = {https://www.arthurperret.fr/cours/format-texte.html},
|
||||
urldate = {2023-04-18},
|
||||
abstract = {Cette page explique ce qu’est le format texte et donne des arguments en faveur de son utilisation. Elle ouvre vers d’autres ressources pour explorer l’écosystème du format texte.},
|
||||
langid = {fre},
|
||||
keywords = {cmu,markdown,non lu,plain text},
|
||||
file = {/home/igor/Zotero/storage/3IM8K4DU/format-texte.html}
|
||||
}
|
||||
|
||||
@article{perretMarkdown2022,
|
||||
title = {Markdown},
|
||||
author = {Perret, Arthur},
|
||||
date = {2022-12-11},
|
||||
journaltitle = {Arthur Perret},
|
||||
publisher = {arthurperret.fr/},
|
||||
url = {https://www.arthurperret.fr/cours/markdown.html},
|
||||
urldate = {2023-04-17},
|
||||
abstract = {Cette page explique ce qu’est Markdown, le plus populaire des langages de balisage léger, et renvoie vers un tutoriel interactif en français.},
|
||||
langid = {french},
|
||||
keywords = {cmu,documentation,markdown,non lu},
|
||||
file = {/home/igor/Zotero/storage/HZNSDQ7S/markdown.html}
|
||||
}
|
||||
|
||||
@online{perretMarkdownTraitementTexte2022,
|
||||
title = {Markdown et traitement de texte~: une méthode pour collaborer},
|
||||
shorttitle = {Markdown et traitement de texte},
|
||||
author = {Perret, Arthur},
|
||||
date = {2022-10-25},
|
||||
url = {https://www.arthurperret.fr/blog/2022-10-25-markdown-traitement-de-texte-methode-pour-collaborer.html},
|
||||
urldate = {2024-04-23},
|
||||
langid = {fre},
|
||||
organization = {arthurperret.fr},
|
||||
keywords = {non lu},
|
||||
file = {/home/igor/Zotero/storage/TQEHEIHA/2022-10-25-markdown-traitement-de-texte-methode-pour-collaborer.html}
|
||||
}
|
||||
|
||||
@software{pollardTemplateWritingPhD2023,
|
||||
title = {Template for Writing a {{PhD}} Thesis in {{Markdown}}},
|
||||
author = {Pollard, Tom},
|
||||
date = {2023-04-17T04:40:26Z},
|
||||
origdate = {2015-02-10T10:32:25Z},
|
||||
url = {https://github.com/tompollard/phd_thesis_markdown},
|
||||
urldate = {2023-04-17},
|
||||
abstract = {Template for writing a PhD thesis in Markdown},
|
||||
keywords = {cmu,markdown,non lu,pandoc,Publication scientifique,thesis-template}
|
||||
}
|
||||
|
||||
@article{schneiderFacilitatingOpenScience2022,
|
||||
title = {Facilitating Open Science Practices for Research Syntheses: {{PreregRS}} Guides Preregistration.},
|
||||
author = {Schneider, Jürgen and Backfisch, Iris and Lachner, Andreas},
|
||||
date = {2022-03},
|
||||
journaltitle = {Res Synth Methods},
|
||||
volume = {13},
|
||||
number = {2},
|
||||
eprint = {34921744},
|
||||
eprinttype = {pmid},
|
||||
pages = {284--289},
|
||||
location = {England},
|
||||
issn = {1759-2887 1759-2879},
|
||||
doi = {10.1002/jrsm.1540},
|
||||
abstract = {Researchers increasingly engage in adopting open science practices in the field of research syntheses, such as preregistration. Preregistration is a central open science practice in empirical research to enhance transparency in the research process and it gains steady adoption in the context of conducting research synthesis. From an interdisciplinary perspective, frameworks and particularly templates are lacking which support researchers preparing a preregistration. To this end, we introduce preregRS, a template to guide researchers across disciplines through the process of preregistering research syntheses. We utilized an R Markdown template file to provide a framework that structures the process of preparing a preregistration. Researchers can write up the preregistration using the template file similar to filling out a form, with the template providing additional hints and further information for the decisions along the framework. We integrated the R Markdown template in an R package for easy installation and use, but also provide a browser-based option for users granting low-barrier access. PreregRS constitutes a first step to facilitate and support preregistration with research syntheses for all disciplines. It further adds to establishing open science practices in conducting research syntheses.},
|
||||
langid = {english},
|
||||
keywords = {*Surveys and Questionnaires,cmu,Empirical Research,markdown,non lu,open science,preregistration,pubmed,R markdown,R package}
|
||||
}
|
||||
|
||||
@article{yuVeridicalDataScience2020,
|
||||
title = {Veridical Data Science.},
|
||||
author = {Yu, Bin and Kumbier, Karl},
|
||||
date = {2020-02-25},
|
||||
journaltitle = {Proc Natl Acad Sci U S A},
|
||||
volume = {117},
|
||||
number = {8},
|
||||
eprint = {32054788},
|
||||
eprinttype = {pmid},
|
||||
pages = {3920--3929},
|
||||
location = {United States},
|
||||
issn = {1091-6490 0027-8424},
|
||||
doi = {10.1073/pnas.1901326117},
|
||||
abstract = {Building and expanding on principles of statistics, machine learning, and scientific inquiry, we propose the predictability, computability, and stability (PCS) framework for veridical data science. Our framework, composed of both a workflow and documentation, aims to provide responsible, reliable, reproducible, and transparent results across the data science life cycle. The PCS workflow uses predictability as a reality check and considers the importance of computation in data collection/storage and algorithm design. It augments predictability and computability with an overarching stability principle. Stability expands on statistical uncertainty considerations to assess how human judgment calls impact data results through data and model/algorithm perturbations. As part of the PCS workflow, we develop PCS inference procedures, namely PCS perturbation intervals and PCS hypothesis testing, to investigate the stability of data results relative to problem formulation, data cleaning, modeling decisions, and interpretations. We illustrate PCS inference through neuroscience and genomics projects of our own and others. Moreover, we demonstrate its favorable performance over existing methods in terms of receiver operating characteristic (ROC) curves in high-dimensional, sparse linear model simulations, including a wide range of misspecified models. Finally, we propose PCS documentation based on R Markdown or Jupyter Notebook, with publicly available, reproducible codes and narratives to back up human choices made throughout an analysis. The PCS workflow and documentation are demonstrated in a genomics case study available on Zenodo.},
|
||||
langid = {english},
|
||||
pmcid = {PMC7049126},
|
||||
keywords = {cmu,computation,data science,markdown,non lu,prediction,pubmed,R markdown,stability},
|
||||
file = {/home/igor/Zotero/storage/GWVCYDA6/Yu_Kumbier_2020_Veridical data science.pdf}
|
||||
}
|
||||
|
|
@ -7,13 +7,13 @@
|
|||
eprint = {35252947},
|
||||
eprinttype = {pmid},
|
||||
pages = {22--30},
|
||||
location = {{Netherlands}},
|
||||
location = {Netherlands},
|
||||
issn = {2667-145X 2667-1468},
|
||||
doi = {10.1016/j.jmsacl.2022.02.004},
|
||||
abstract = {BACKGROUND: Indirect reference intervals require robust statistical approaches to separate the pathological and healthy values. This can be achieved with a data pipeline created in R, a freely available statistical programming language. METHODS: A data pipeline was created to ingest, partition, normalize, remove outliers, and identify reference intervals for testosterone (Testo; n ~=~7,207) and aspartate aminotransferase (AST; n ~=~5,882) using data sets from NHANES. RESULTS: The estimates for AST and Testo determined by this pipeline approximated current RIs. Care should be taken when using this pipeline as there are limitations that depend on the pathology of the analyte and the data set being used for RI estimation. CONCLUSIONS: R can be used to create a robust statistical reference interval pipeline.},
|
||||
langid = {english},
|
||||
pmcid = {PMC8889237},
|
||||
keywords = {ANOVA; Analysis of variance,AST; aspartate aminotransferase,CLSI; Clinical Laboratory Standards Institute,cmu,EHR; electronic health record,IFCC; International Federation of Clinical Chemistry and Laboratory Medicine,LC-MS/MS; Liquid chromatography tandem mass spectrometry,LIS; Laboratory informatics system,markdown,Mixtools,non lu,pubmed,R markdown,R markdown tutorial,Reference interval,RI; reference interval,SDI; Standard deviation index,SDR; Standard deviation ratio,Testo; Testosterone,TukeyHSD; Tukey multiple pairwise-comparisons,z5; Critical z-score},
|
||||
keywords = {ANOVA Analysis of variance,AST aspartate aminotransferase,CLSI Clinical Laboratory Standards Institute,cmu,EHR electronic health record,IFCC International Federation of Clinical Chemistry and Laboratory Medicine,LC-MS/MS Liquid chromatography tandem mass spectrometry,LIS Laboratory informatics system,markdown,Mixtools,non lu,pubmed,R markdown,R markdown tutorial,Reference interval,RI reference interval,SDI Standard deviation index,SDR Standard deviation ratio,Testo Testosterone,TukeyHSD Tukey multiple pairwise-comparisons,z5 Critical z-score},
|
||||
file = {/home/igor/Zotero/storage/YYP9JQTY/Bunch_2022_Indirect reference intervals using an R pipeline.pdf}
|
||||
}
|
||||
|
||||
|
|
@ -27,7 +27,7 @@
|
|||
eprint = {35657454},
|
||||
eprinttype = {pmid},
|
||||
pages = {59},
|
||||
location = {{Germany}},
|
||||
location = {Germany},
|
||||
issn = {2509-8020},
|
||||
doi = {10.1186/s41687-022-00464-9},
|
||||
abstract = {BACKGROUND: The Patient-Reported Outcome Measurement Information System(®) (PROMIS(®)) was developed to reliably measure health-related quality of life using the patient's voice. To achieve these aims, PROMIS utilized Item Response Theory methods in its development, validation and implementation. PROMIS measures are typically scored using a specific method to calculate scores, called Expected A Posteriori estimation. BODY: Expected A Posteriori scoring methods are flexible, produce accurate scores and can be efficiently calculated by statistical software. This work seeks to make Expected A Posteriori scoring methods transparent and accessible to a larger audience through description, graphical demonstration and examples. Further applications and practical considerations of Expected A Posteriori scoring are presented and discussed. All materials used in this paper are made available through the R Markdown reproducibility framework and are intended to be reviewed and reused. Commented statistical code for the calculation of Expected A Posteriori scores is included. CONCLUSION: This work seeks to provide the reader with a summary and visualization of the operation of Expected A Posteriori scoring, as implemented in PROMIS. As PROMIS is increasingly adopted and implemented, this work will provide a basis for making psychometric methods more accessible to the PROMIS user base.},
|
||||
|
|
@ -43,8 +43,8 @@
|
|||
url = {https://commonmark.org/},
|
||||
urldate = {2023-04-25},
|
||||
langid = {english},
|
||||
organization = {{CommonMark}},
|
||||
keywords = {non lu},
|
||||
organization = {CommonMark},
|
||||
keywords = {cmu,non lu},
|
||||
file = {/home/igor/Zotero/storage/ESNTHT9H/commonmark.org.html}
|
||||
}
|
||||
|
||||
|
|
@ -57,7 +57,7 @@
|
|||
number = {3},
|
||||
eprint = {30841575},
|
||||
eprinttype = {pmid},
|
||||
location = {{Switzerland}},
|
||||
location = {Switzerland},
|
||||
issn = {2218-1989},
|
||||
doi = {10.3390/metabo9030043},
|
||||
abstract = {Despite the proposal of minimum reporting guidelines for metabolomics over a decade ago, reporting on the data analysis step in metabolomics studies has been shown to be unclear and incomplete. Major omissions and a lack of logical flow render the data analysis' sections in metabolomics studies impossible to follow, and therefore replicate or even imitate. Here, we propose possible reasons why the original reporting guidelines have had poor adherence and present an approach to improve their uptake. We present in this paper an R markdown reporting template file that guides the production of text and generates workflow diagrams based on user input. This R Markdown template contains, as an example in this instance, a set of minimum information requirements specifically for the data pre-treatment and data analysis section of biomarker discovery metabolomics studies, (gleaned directly from the original proposed guidelines by Goodacre at al). These minimum requirements are presented in the format of a questionnaire checklist in an R markdown template file. The R Markdown reporting template proposed here can be presented as a starting point to encourage the data analysis section of a metabolomics manuscript to have a more logical presentation and to contain enough information to be understandable and reusable. The idea is that these guidelines would be open to user feedback, modification and updating by the metabolomics community via GitHub.},
|
||||
|
|
@ -76,7 +76,7 @@
|
|||
eprint = {35452633},
|
||||
eprinttype = {pmid},
|
||||
pages = {108822},
|
||||
location = {{United States}},
|
||||
location = {United States},
|
||||
issn = {1879-3134 0025-5564},
|
||||
doi = {10.1016/j.mbs.2022.108822},
|
||||
abstract = {In this article we show how dynamic publication media and the COPASI R Connector (CoRC) can be combined in a natural and synergistic way to communicate (biochemical) models. Dynamic publication media are becoming a popular tool for authors to effectively compose and publish their work. They are built from templates and the final documents are created dynamically. In addition, they can also be interactive. Working with dynamic publication media is made easy with the programming environment R via its integration with tools such as R Markdown, Jupyter and Shiny. Additionally, the COmplex PAthway SImulator COPASI (http://www.copasi.org), a widely used biochemical modelling toolkit, is available in R through the use of the COPASI R Connector (CoRC, https://jpahle.github.io/CoRC). Models are a common tool in the mathematical biosciences, in particular kinetic models of biochemical networks in (computational) systems biology. We focus on three application areas of dynamic publication media and CoRC: Documentation (reproducible workflows), Teaching (creating self-paced lessons) and Science Communication (immersive and engaging presentation). To illustrate these, we created six dynamic document examples in the form of R Markdown and Jupyter notebooks, hosted on the platforms GitHub, shinyapps.io, Google Colaboratory. Having code and output in one place, creating documents in template-form and the option of interactivity make the combination of dynamic documents and CoRC a versatile tool. All our example documents are freely available at https://jpahle.github.io/DynamiCoRC under the Creative Commons BY 4.0 licence.},
|
||||
|
|
@ -94,8 +94,8 @@
|
|||
urldate = {2023-04-17},
|
||||
eventtitle = {So-Mate 2022},
|
||||
langid = {fre},
|
||||
venue = {{Pau}},
|
||||
keywords = {markdown,non lu,pandoc,Publication scientifique}
|
||||
venue = {Pau},
|
||||
keywords = {cmu,markdown,non lu,pandoc,Publication scientifique}
|
||||
}
|
||||
|
||||
@online{eyssetteUtiliserMarkdownPour2023,
|
||||
|
|
@ -107,8 +107,8 @@
|
|||
urldate = {2023-04-17},
|
||||
abstract = {Utiliser le Markdown pour tout faire.Le diaporama (fait en markdown bien sûr !) qui m'a servi de support lors de mon atelier pour la Journée du Libre Éducatif 2023.https://eyssette.forge.aeif.fr/marp-slides/slides/2022-2023/utiliser-le-markdown-pour-tout-faire\#Markdown\#JDLE\#JDLE2023\#TeamEduc\#MastoProf},
|
||||
langid = {french},
|
||||
organization = {{Mastodon}},
|
||||
keywords = {fediverse,markdown,mastodon,non lu},
|
||||
organization = {Mastodon},
|
||||
keywords = {cmu,fediverse,markdown,mastodon,non lu},
|
||||
file = {/home/igor/Zotero/storage/7FYFNED6/110158455766516456.html}
|
||||
}
|
||||
|
||||
|
|
@ -119,7 +119,7 @@
|
|||
url = {https://eyssette.forge.aeif.fr/marp-slides/slides/2022-2023/utiliser-le-markdown-pour-tout-faire},
|
||||
urldate = {2023-04-17},
|
||||
langid = {fre},
|
||||
keywords = {non lu},
|
||||
keywords = {cmu,non lu},
|
||||
file = {/home/igor/Zotero/storage/I7CTE3X5/utiliser-le-markdown-pour-tout-faire.html}
|
||||
}
|
||||
|
||||
|
|
@ -132,8 +132,8 @@
|
|||
urldate = {2023-04-17},
|
||||
abstract = {Un guide simple pour apprendre Markdown.},
|
||||
langid = {fre},
|
||||
organization = {{flus}},
|
||||
keywords = {documentation,markdown,non lu},
|
||||
organization = {flus},
|
||||
keywords = {cmu,documentation,markdown,non lu},
|
||||
file = {/home/igor/Zotero/storage/96VGWVYV/markdown.html}
|
||||
}
|
||||
|
||||
|
|
@ -146,7 +146,7 @@
|
|||
eprint = {35623397},
|
||||
eprinttype = {pmid},
|
||||
pages = {108844},
|
||||
location = {{United States}},
|
||||
location = {United States},
|
||||
issn = {1879-3134 0025-5564},
|
||||
doi = {10.1016/j.mbs.2022.108844},
|
||||
abstract = {Advancing technologies, including interactive tools, are changing classroom pedagogy across academia. Here, we discuss the R Markdown interface, which allows for the creation of partial or complete interactive classroom modules for courses using the R programming language. R Markdown files mix sections of R code with formatted text, including LaTeX, which are rendered together to form complete reports and documents. These features allow instructors to create classroom modules that guide students through concepts, while providing areas for coding and text response by students. Students can also learn to create their own reports for more independent assignments. After presenting the features and uses of R Markdown to enhance teaching and learning, we present examples of materials from two courses. In a Computational Modeling course for math students, we used R Markdown to guide students through exploring mathematical models to understand the principle of herd immunity. In a Data Visualization and Communication course for biology students, we used R Markdown for teaching the fundamentals of R programming and graphing, and for students to learn to create reproducible data investigations. Through these examples, we demonstrate the benefits of R Markdown as a dynamic teaching and learning tool.},
|
||||
|
|
@ -164,8 +164,8 @@
|
|||
url = {https://daringfireball.net/projects/markdown/},
|
||||
urldate = {2023-04-17},
|
||||
langid = {english},
|
||||
organization = {{Daring Fireball}},
|
||||
keywords = {documentation,markdown,non lu},
|
||||
organization = {Daring Fireball},
|
||||
keywords = {cmu,documentation,markdown,non lu},
|
||||
file = {/home/igor/Zotero/storage/J7WP5B3D/markdown.html}
|
||||
}
|
||||
|
||||
|
|
@ -179,7 +179,7 @@
|
|||
eprint = {34196689},
|
||||
eprinttype = {pmid},
|
||||
pages = {3914--3915},
|
||||
location = {{England}},
|
||||
location = {England},
|
||||
issn = {1367-4811 1367-4803},
|
||||
doi = {10.1093/bioinformatics/btab459},
|
||||
abstract = {MOTIVATION: Genome browsers are an essential tool in genome analysis. Modern genome browsers enable complex and interactive visualization of a wide variety of genomic data modalities. While such browsers are very powerful, they can be challenging to configure and program for bioinformaticians lacking expertise in web development. RESULTS: We have developed an R package that provides an interface to the JBrowse 2 genome browser. The package can be used to configure and customize the browser entirely with R code. The browser can be deployed from the R console, or embedded in Shiny applications or R Markdown documents. AVAILABILITY AND IMPLEMENTATION: JBrowseR is available for download from CRAN, and the source code is openly available from the Github repository at https://github.com/GMOD/JBrowseR/.},
|
||||
|
|
@ -198,12 +198,12 @@
|
|||
eprint = {34742775},
|
||||
eprinttype = {pmid},
|
||||
pages = {113176},
|
||||
location = {{Netherlands}},
|
||||
location = {Netherlands},
|
||||
issn = {1872-7905 0022-1759},
|
||||
doi = {10.1016/j.jim.2021.113176},
|
||||
abstract = {Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed to guide the investigation. Thus, there is an increasing need to develop applications geared towards bench-scientists to help them abstract the technical challenges of the analysis so that they can focus on the science at play. It is also expected that such applications should support closer collaboration between bioinformaticians and bench-scientists by providing reproducible science tools. We present SCHNAPPs, a Graphical User Interface (GUI), designed to enable bench-scientists to autonomously explore and interpret scRNAseq data and associated annotations. The R/Shiny-based application allows following different steps of scRNAseq analysis workflows from Seurat or Scran packages: performing quality control on cells and genes, normalizing the expression matrix, integrating different samples, dimension reduction, clustering, and differential gene expression analysis. Visualization tools for exploring each step of the process include violin plots, 2D projections, Box-plots, alluvial plots, and histograms. An R-markdown report can be generated that tracks modifications and selected visualizations. The modular design of the tool allows it to easily integrate new visualizations and analyses by bioinformaticians. We illustrate the main features of the tool by applying it to the characterization of T cells in a scRNAseq and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) experiment of two healthy individuals.},
|
||||
langid = {english},
|
||||
keywords = {*Sequence Analysis; RNA,*Single-Cell Analysis,*Software,CITE-Seq,cmu,Humans,Leukocytes; Mononuclear/*cytology/immunology,markdown,multi-omics data analysis,non lu,pubmed,R markdown,scRNA-seq,Shiny application},
|
||||
keywords = {*Sequence Analysis RNA,*Single-Cell Analysis,*Software,CITE-Seq,cmu,Humans,Leukocytes Mononuclear/*cytology/immunology,markdown,multi-omics data analysis,non lu,pubmed,R markdown,scRNA-seq,Shiny application},
|
||||
file = {/home/igor/Zotero/storage/PEARJ76P/Jagla et al_2021_SCHNAPPs - Single Cell sHiNy APPlication(s).pdf}
|
||||
}
|
||||
|
||||
|
|
@ -217,7 +217,7 @@
|
|||
eprint = {34988439},
|
||||
eprinttype = {pmid},
|
||||
pages = {lqab116},
|
||||
location = {{England}},
|
||||
location = {England},
|
||||
issn = {2631-9268},
|
||||
doi = {10.1093/nargab/lqab116},
|
||||
abstract = {Glimma 1.0 introduced intuitive, point-and-click interactive graphics for differential gene expression analysis. Here, we present a major update to Glimma that brings improved interactivity and reproducibility using high-level visualization frameworks for R and JavaScript. Glimma 2.0 plots are now readily embeddable in R Markdown, thus allowing users to create reproducible reports containing interactive graphics. The revamped multidimensional scaling plot features dashboard-style controls allowing the user to dynamically change the colour, shape and size of sample points according to different experimental conditions. Interactivity was enhanced in the MA-style plot for comparing differences to average expression, which now supports selecting multiple genes, export options to PNG, SVG or CSV formats and includes a new volcano plot function. Feature-rich and user-friendly, Glimma makes exploring data for gene expression analysis more accessible and intuitive and is available on Bioconductor and GitHub.},
|
||||
|
|
@ -227,6 +227,44 @@
|
|||
file = {/home/igor/Zotero/storage/ZQD2WXNN/Kariyawasam et al_2021_Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready.pdf}
|
||||
}
|
||||
|
||||
@online{masuttiRedigerManipulerDocuments2019,
|
||||
title = {Rédiger et manipuler des documents avec Markdown},
|
||||
author = {Masutti, Christophe},
|
||||
date = {2019-05-08},
|
||||
url = {https://golb.statium.link/post/20190528rediger-et-manipuler-des-documents-markdown/},
|
||||
urldate = {2024-03-19},
|
||||
langid = {fre},
|
||||
organization = {Statium : blog},
|
||||
keywords = {cmu,markdown,non lu,pandoc,publication numérique,Publication scientifique}
|
||||
}
|
||||
|
||||
@article{ovadiaMarkdownLibrariansAcademics2014a,
|
||||
title = {Markdown for {{Librarians}} and {{Academics}}},
|
||||
author = {Ovadia, Steven},
|
||||
date = {2014-04-03},
|
||||
journaltitle = {Behavioral \& Social Sciences Librarian},
|
||||
volume = {33},
|
||||
number = {2},
|
||||
pages = {120--124},
|
||||
issn = {0163-9269, 1544-4546},
|
||||
doi = {10.1080/01639269.2014.904696},
|
||||
url = {http://www.tandfonline.com/doi/abs/10.1080/01639269.2014.904696},
|
||||
urldate = {2023-05-02},
|
||||
langid = {english},
|
||||
keywords = {cmu,markdown,non lu,Publication scientifique},
|
||||
file = {/home/igor/Zotero/storage/25MP4P3N/Ovadia_2014_Markdown for Librarians and Academics.pdf}
|
||||
}
|
||||
|
||||
@online{paged.jsPagedJs,
|
||||
title = {About {{Paged}}.Js?},
|
||||
author = {Paged.js},
|
||||
url = {https://pagedjs.org/about/},
|
||||
urldate = {2024-03-08},
|
||||
langid = {english},
|
||||
organization = {Paged.js},
|
||||
keywords = {édition numérique,non lu,publication numérique}
|
||||
}
|
||||
|
||||
@online{pandocWritingThesisThinking2023,
|
||||
type = {Mastodon post},
|
||||
title = {Writing a \#thesis? {{Thinking}} about Doing It in \#{{Markdown}}? {{No}} Problem, {{Tom Pollard}} Has You Covered.{{https://github.com/tompollard/phd\_thesis\_ma…}}},
|
||||
|
|
@ -237,46 +275,51 @@
|
|||
urldate = {2023-04-17},
|
||||
abstract = {Writing a \#thesis? Thinking about doing it in \#Markdown? No problem, Tom Pollard has you covered.https://github.com/tompollard/phd\_thesis\_markdown},
|
||||
langid = {english},
|
||||
organization = {{Mastodon}},
|
||||
keywords = {fediverse,markdown,mastodon,non lu,pandoc,Publication scientifique},
|
||||
organization = {Mastodon},
|
||||
keywords = {cmu,fediverse,markdown,mastodon,non lu,pandoc,Publication scientifique},
|
||||
file = {/home/igor/Zotero/storage/T354LYSW/110184589069297715.html}
|
||||
}
|
||||
|
||||
@online{perretFormatTexte2022,
|
||||
type = {Site personnel},
|
||||
@article{perretFormatTexte2022,
|
||||
title = {Format texte},
|
||||
author = {Perret, Arthur},
|
||||
date = {2022-12-11},
|
||||
journaltitle = {Arthur Perret},
|
||||
url = {https://www.arthurperret.fr/cours/format-texte.html},
|
||||
urldate = {2023-04-18},
|
||||
abstract = {Cette page explique ce qu’est le format texte et donne des arguments en faveur de son utilisation. Elle ouvre vers d’autres ressources pour explorer l’écosystème du format texte.},
|
||||
langid = {fre},
|
||||
organization = {{Arthur Perret}},
|
||||
keywords = {markdown,non lu,plain text},
|
||||
note = {\begin{quotation}
|
||||
|
||||
\par
|
||||
[C]’est un fichier qui ne contient des caractères. (Perret, 2022)
|
||||
\par
|
||||
\end{quotation}},
|
||||
keywords = {cmu,markdown,non lu,plain text},
|
||||
file = {/home/igor/Zotero/storage/3IM8K4DU/format-texte.html}
|
||||
}
|
||||
|
||||
@online{perretMarkdown2022,
|
||||
type = {Site personnel},
|
||||
@article{perretMarkdown2022,
|
||||
title = {Markdown},
|
||||
author = {Perret, Arthur},
|
||||
date = {2022-12-11},
|
||||
publisher = {{arthurperret.fr/}},
|
||||
journaltitle = {Arthur Perret},
|
||||
publisher = {arthurperret.fr/},
|
||||
url = {https://www.arthurperret.fr/cours/markdown.html},
|
||||
urldate = {2023-04-17},
|
||||
abstract = {Cette page explique ce qu’est Markdown, le plus populaire des langages de balisage léger, et renvoie vers un tutoriel interactif en français.},
|
||||
langid = {french},
|
||||
organization = {{Arthur Perret}},
|
||||
keywords = {documentation,markdown,non lu},
|
||||
keywords = {cmu,documentation,markdown,non lu},
|
||||
file = {/home/igor/Zotero/storage/HZNSDQ7S/markdown.html}
|
||||
}
|
||||
|
||||
@online{perretMarkdownTraitementTexte2022,
|
||||
title = {Markdown et traitement de texte~: une méthode pour collaborer},
|
||||
shorttitle = {Markdown et traitement de texte},
|
||||
author = {Perret, Arthur},
|
||||
date = {2022-10-25},
|
||||
url = {https://www.arthurperret.fr/blog/2022-10-25-markdown-traitement-de-texte-methode-pour-collaborer.html},
|
||||
urldate = {2024-04-23},
|
||||
langid = {fre},
|
||||
organization = {arthurperret.fr},
|
||||
keywords = {non lu},
|
||||
file = {/home/igor/Zotero/storage/TQEHEIHA/2022-10-25-markdown-traitement-de-texte-methode-pour-collaborer.html}
|
||||
}
|
||||
|
||||
@software{pollardTemplateWritingPhD2023,
|
||||
title = {Template for Writing a {{PhD}} Thesis in {{Markdown}}},
|
||||
author = {Pollard, Tom},
|
||||
|
|
@ -285,7 +328,7 @@
|
|||
url = {https://github.com/tompollard/phd_thesis_markdown},
|
||||
urldate = {2023-04-17},
|
||||
abstract = {Template for writing a PhD thesis in Markdown},
|
||||
keywords = {markdown,non lu,pandoc,Publication scientifique,thesis-template}
|
||||
keywords = {cmu,markdown,non lu,pandoc,Publication scientifique,thesis-template}
|
||||
}
|
||||
|
||||
@article{schneiderFacilitatingOpenScience2022,
|
||||
|
|
@ -298,7 +341,7 @@
|
|||
eprint = {34921744},
|
||||
eprinttype = {pmid},
|
||||
pages = {284--289},
|
||||
location = {{England}},
|
||||
location = {England},
|
||||
issn = {1759-2887 1759-2879},
|
||||
doi = {10.1002/jrsm.1540},
|
||||
abstract = {Researchers increasingly engage in adopting open science practices in the field of research syntheses, such as preregistration. Preregistration is a central open science practice in empirical research to enhance transparency in the research process and it gains steady adoption in the context of conducting research synthesis. From an interdisciplinary perspective, frameworks and particularly templates are lacking which support researchers preparing a preregistration. To this end, we introduce preregRS, a template to guide researchers across disciplines through the process of preregistering research syntheses. We utilized an R Markdown template file to provide a framework that structures the process of preparing a preregistration. Researchers can write up the preregistration using the template file similar to filling out a form, with the template providing additional hints and further information for the decisions along the framework. We integrated the R Markdown template in an R package for easy installation and use, but also provide a browser-based option for users granting low-barrier access. PreregRS constitutes a first step to facilitate and support preregistration with research syntheses for all disciplines. It further adds to establishing open science practices in conducting research syntheses.},
|
||||
|
|
@ -316,7 +359,7 @@
|
|||
eprint = {32054788},
|
||||
eprinttype = {pmid},
|
||||
pages = {3920--3929},
|
||||
location = {{United States}},
|
||||
location = {United States},
|
||||
issn = {1091-6490 0027-8424},
|
||||
doi = {10.1073/pnas.1901326117},
|
||||
abstract = {Building and expanding on principles of statistics, machine learning, and scientific inquiry, we propose the predictability, computability, and stability (PCS) framework for veridical data science. Our framework, composed of both a workflow and documentation, aims to provide responsible, reliable, reproducible, and transparent results across the data science life cycle. The PCS workflow uses predictability as a reality check and considers the importance of computation in data collection/storage and algorithm design. It augments predictability and computability with an overarching stability principle. Stability expands on statistical uncertainty considerations to assess how human judgment calls impact data results through data and model/algorithm perturbations. As part of the PCS workflow, we develop PCS inference procedures, namely PCS perturbation intervals and PCS hypothesis testing, to investigate the stability of data results relative to problem formulation, data cleaning, modeling decisions, and interpretations. We illustrate PCS inference through neuroscience and genomics projects of our own and others. Moreover, we demonstrate its favorable performance over existing methods in terms of receiver operating characteristic (ROC) curves in high-dimensional, sparse linear model simulations, including a wide range of misspecified models. Finally, we propose PCS documentation based on R Markdown or Jupyter Notebook, with publicly available, reproducible codes and narratives to back up human choices made throughout an analysis. The PCS workflow and documentation are demonstrated in a genomics case study available on Zenodo.},
|
||||
|
|
|
|||
152
style.css
152
style.css
|
|
@ -1,21 +1,16 @@
|
|||
@media print {
|
||||
body {
|
||||
font-family: TheSansOsF-Plain, "Open Sans", Arial, Helvetica, sans-serif;
|
||||
counter-reset: figureNumber;
|
||||
}
|
||||
/* Définit que string(date) contient la date */
|
||||
.date {
|
||||
string-set: date content(text);
|
||||
display: none;
|
||||
}
|
||||
/* Définit que running(licenceBlock) contient le block licence */
|
||||
#licence {
|
||||
position: running(licenceBlock);
|
||||
}
|
||||
|
||||
/* **************************
|
||||
* Définition des pages *
|
||||
* ************************ */
|
||||
|
||||
@page {
|
||||
size: A4;
|
||||
margin: 25mm 0;
|
||||
margin: 25mm;
|
||||
bleed: 6mm;
|
||||
/* Numérotation de page au centre en bas
|
||||
* de la page. Le compteur est définit
|
||||
* dans le selecteur body. */
|
||||
@bottom-center {
|
||||
content: counter(page);
|
||||
}
|
||||
|
|
@ -29,6 +24,8 @@
|
|||
margin-right: 25mm;
|
||||
}
|
||||
@page:first {
|
||||
/* Insertion en haut à droite du logo de la
|
||||
* bibliothèque de l'UNIGE. */
|
||||
@top-right {
|
||||
content: "";
|
||||
background-image: url("./static/bibliotheque-logo.svg");
|
||||
|
|
@ -36,6 +33,9 @@
|
|||
background-repeat: no-repeat;
|
||||
background-size: 25%;
|
||||
}
|
||||
/* Place le bloc de la licence en bas à gauche
|
||||
* de la première page. Voir le sélecteur
|
||||
* #licence plus bas. */
|
||||
@bottom-left{
|
||||
content: element(licenceBlock);
|
||||
font-size: small;
|
||||
|
|
@ -43,29 +43,57 @@
|
|||
@bottom-center {
|
||||
content: none;
|
||||
}
|
||||
/* Insert la date en bas à droite de la
|
||||
* première page. Voir le sélecteur .date */
|
||||
@bottom-right {
|
||||
content: string(date);
|
||||
font-size: small;
|
||||
}
|
||||
}
|
||||
@page:nth(11) {
|
||||
@bottom-center {
|
||||
content: none;
|
||||
|
||||
/* **************************
|
||||
* Définitions globales *
|
||||
* ************************ */
|
||||
|
||||
body {
|
||||
font-family: "TheSansOsF", "Open Sans", Arial, Helvetica, sans-serif;
|
||||
/* Définit les deux variable de compteur nécessaires */
|
||||
counter-reset: figureNumber toc;
|
||||
}
|
||||
/* Définit que string(date) contient la date indiquée dans le frontmatter
|
||||
* de la source markdown */
|
||||
.date {
|
||||
string-set: date content(text);
|
||||
display: none; /* Pour ne pas afficher la date sous le titre. */
|
||||
}
|
||||
h2 {
|
||||
color: #d80669;
|
||||
text-decoration: underline;
|
||||
/* Définit que running(licenceBlock) contient le block licence.
|
||||
* Le bloc licence est décrit dans le fichier markdown source, au-dessous
|
||||
* de la section des objectifs. Le CSS permet de le placer correctement */
|
||||
#licence {
|
||||
position: running(licenceBlock);
|
||||
}
|
||||
#1st-section,
|
||||
#bibliographie,
|
||||
.footnotes {
|
||||
break-before: page;
|
||||
|
||||
/* *****************
|
||||
* Page de titre *
|
||||
* *************** */
|
||||
|
||||
.logo {
|
||||
display: inline-flex;
|
||||
justify-content: center;
|
||||
width: 60%;
|
||||
margin: 2em auto 1em auto;
|
||||
}
|
||||
.logo img {
|
||||
max-width: 50%;
|
||||
padding: .5em;
|
||||
}
|
||||
|
||||
#title-block-header {
|
||||
/* Concerne le bloc titre sur la page de titre */
|
||||
text-align: center;
|
||||
margin: 2em 0 6em 0;
|
||||
margin: 4em 0;
|
||||
}
|
||||
|
||||
.authors {
|
||||
display: flex;
|
||||
justify-content: center;
|
||||
|
|
@ -74,14 +102,56 @@
|
|||
margin: 0;
|
||||
padding: 0 1em;
|
||||
}
|
||||
|
||||
/* Les 4 règles suivantes mettent en forme la table des matières :*
|
||||
* Suppression des liste à puce, numérotation des chapitres et affichage du
|
||||
* numéro de page. */
|
||||
#TOC ul {
|
||||
list-style: none;
|
||||
counter-reset: toc;
|
||||
padding-left: 1.5em;
|
||||
}
|
||||
#TOC li {
|
||||
counter-increment: toc;
|
||||
}
|
||||
#TOC li::before {
|
||||
content: counter(toc) ". ";
|
||||
}
|
||||
#TOC a::after {
|
||||
content: target-counter(attr(href url), page);
|
||||
position: absolute;
|
||||
right: 0;
|
||||
}
|
||||
|
||||
/* ***************************
|
||||
* Structure du document *
|
||||
* ************************* */
|
||||
|
||||
/* Ajouter ou supprimer les ID de titre pour un saut de page
|
||||
* Les IDs #first-section et #bibliography peuvent être ajoutés
|
||||
* dans la source markdown. */
|
||||
#first-section,
|
||||
#bibliography,
|
||||
.footnotes {
|
||||
break-before: page;
|
||||
}
|
||||
|
||||
h2 {
|
||||
color: #d80669;
|
||||
text-decoration: underline;
|
||||
}
|
||||
|
||||
pre {
|
||||
font-family:'Courier New', Courier, monospace;
|
||||
font-size: 90%;
|
||||
background-color: #f2f1f1;
|
||||
border: 2px solid #d80669;
|
||||
border-radius: .5em;
|
||||
margin: 1em;
|
||||
padding: .5em 1em;
|
||||
/* Évite que les blocs de code ne soient séparés sur 2 pages */
|
||||
break-inside: avoid;
|
||||
}
|
||||
pre > code {
|
||||
border-radius: none;
|
||||
padding: none;
|
||||
}
|
||||
code {
|
||||
font-family:'Courier New', Courier, monospace;
|
||||
|
|
@ -90,6 +160,7 @@
|
|||
padding: 2px;
|
||||
border-radius: 5px;
|
||||
}
|
||||
|
||||
.footnotes::before {
|
||||
content: "Notes";
|
||||
color: #d80669;
|
||||
|
|
@ -99,12 +170,14 @@
|
|||
.footnote-ref {
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
figure {
|
||||
display: flex;
|
||||
flex-direction: column;
|
||||
border: 2px solid #d80669;
|
||||
border-radius: .5em;
|
||||
padding: .5em;
|
||||
break-inside: avoid;
|
||||
}
|
||||
figure img {
|
||||
max-width: 85%;
|
||||
|
|
@ -119,34 +192,15 @@
|
|||
figcaption::before {
|
||||
content: "Figure " counter(figureNumber) " : ";
|
||||
}
|
||||
|
||||
blockquote {
|
||||
font-style: italic;
|
||||
}
|
||||
blockquote em {
|
||||
font-style: normal;
|
||||
}
|
||||
|
||||
div.csl-entry {
|
||||
padding: .5em;
|
||||
}
|
||||
.logo {
|
||||
display: flex;
|
||||
justify-content: center;
|
||||
width: 60%;
|
||||
margin: 2em auto 1em auto;
|
||||
}
|
||||
.logo img {
|
||||
max-width: 50%;
|
||||
padding: .5em;
|
||||
}
|
||||
#TOC ul {
|
||||
list-style: none;
|
||||
counter-reset: tocCounter;
|
||||
padding-left: 1.5em;
|
||||
}
|
||||
#TOC li {
|
||||
counter-increment: tocCounter;
|
||||
}
|
||||
#TOC li::before {
|
||||
content: counter(tocCounter) ". ";
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue