Pseudobulk Analysis with Decoupler and edgeR

topics/single-cell/tutorials/pseudobulk-analysis/data-library.yaml

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+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: single-cell
+  description: Training material for single-cell
+  items:
+  - name: Pseudobulk Analysis with Decoupler and EdgeR
+    items:
+    - name: 'DOI: 10.5281/zenodo.13929549'
+      description: latest
+      items:
+      - url: https://zenodo.org/api/records/13929549/files/Source AnnData file.h5ad/content
+        src: url
+        ext: h5ad
+        info: https://zenodo.org/records/13929549

topics/single-cell/tutorials/pseudobulk-analysis/faqs/index.md

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+---
+layout: faq-page
+---

topics/single-cell/tutorials/pseudobulk-analysis/tutorial.bib

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+@article{Murphy2022,
+  doi = {10.1038/s41467-022-35519-4},
+  url = {https://doi.org/10.1038/s41467-022-35519-4},
+  year = {2022},
+  month = dec,
+  publisher = {Springer Nature},
+  volume = {13},
+  pages = {7851},
+  author = {A.E. Murphy and N.G. Skene},
+  title = {A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis},
+  journal = {Nature Communications}
+}
+
+@article{Squair2021,
+  doi = {10.1038/s41467-021-25960-2},
+  url = {https://doi.org/10.1038/s41467-021-25960-2},
+  year = {2021},
+  month = sep,
+  publisher = {Springer Nature},
+  volume = {12},
+  pages = {5692},
+  author = {Jordan W. Squair and Matthieu Gautier and Claudia Kathe and Mark A. Anderson and Nicholas D. James and Thomas H. Hutson and Rémi Hudelle and Taha Qaiser and Kaya J. E. Matson and Quentin Barraud and Ariel J. Levine and Gioele La Manno and Michael A. Skinnider and Grégoire Courtine},
+  title = {Confronting false discoveries in single-cell differential expression},
+  journal = {Nature Communications}
+}
+
+@article{Badia-iMompel2022,
+  doi = {10.1093/bioadv/vbac016},
+  url = {https://doi.org/10.1093/bioadv/vbac016},
+  year = {2022},
+  volume = {2},
+  number = {1},
+  publisher = {Oxford University Press},
+  author = {Pau Badia-i Mompel and Jose Vélez Santiago and Julia Braunger and Clemens Geiss and Dimitar Dimitrov and Stefan Müller-Dott and Patrick Taus and Antoine Dugourd and Christopher H. Holland and Rodrigo O. Ramirez Flores and Julio Saez-Rodriguez},
+  title = {decoupleR: ensemble of computational methods to infer biological activities from omics data},
+  journal = {Bioinformatics Advances}
+}
+
+@article{Silvin2020,
+  doi = {10.1016/j.cell.2020.08.002},
+  url = {https://doi.org/10.1016/j.cell.2020.08.002},
+  year = {2020},
+  month = sep,
+  publisher = {Elsevier {BV}},
+  volume = {182},
+  number = {6},
+  pages = {1401--1418.e18},
+  author = {A. Silvin and N. Chapuis and G. Dunsmore and A.G. Goubet and A. Dubuisson and L. Derosa and C. Almire and C. H{\'{e}}non and O. Kosmider and N. Droin and P. Rameau and C. Catelain and A. Alfaro and C. Dussiau and C. Friedrich and E. Sourdeau and N. Marin and T.A. Szwebel and D. Cantin and L. Mouthon and D. Borderie and M. Deloger and D. Bredel and S. Mouraud and D. Drubay and M. Andrieu and A.S. Lhonneur and V. Saada and A. Stoclin and C. Willekens and F. Pommeret and F. Griscelli and L.G. Ng and Z. Zhang and P. Bost and I. Amit and F. Barlesi and A. Marabelle and F. P{\`{e}}ne and B. Gachot and F. Andr{\'{e}} and L. Zitvogel and F. Ginhoux and M. Fontenay and E. Solary},
+  title = {Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19},
+  journal = {Cell},
+  pmid = {32810439},
+  pmcid = {PMC7405878}
+}
+
+@article{Liu2015,
+  doi = {10.1093/nar/gkv412},
+  url = {https://doi.org/10.1093/nar/gkv412},
+  year = {2015},
+  month = sep,
+  publisher = {Oxford University Press ({OUP})},
+  volume = {43},
+  number = {15},
+  pages = {e97},
+  author = {Ruijie Liu and Aliaksei Z. Holik and Shian Su and Natasha Jansz and Kelan Chen and Huei San Leong and Marnie E. Blewitt and Marie-Liesse Asselin-Labat and Gordon K. Smyth and Matthew E. Ritchie},
+  title = {Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses},
+  journal = {Nucleic Acids Research}
+}
+
+@online{decoupler-pseudobulk,
+  author = {Saez Lab and Contributors},
+  title = {Pseudobulk Analysis Notebook: A tutorial for pseudobulk analysis using Decoupler},
+  url = {https://github.com/saezlab/decoupler-py/blob/main/docs/source/notebooks/pseudobulk.ipynb},
+  note = {Accessed via Decoupler documentation: \url{https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html}},
+  urldate = {2024-12-09}
+}
+
+@manual{Chen2024,
+  author = {Yunshun Chen and Davis McCarthy and Pedro Baldoni and Matthew Ritchie and Mark Robinson and Gordon Smyth},
+  title = {edgeR User’s Guide},
+  year = {2024},
+  month = oct,
+  edition = {Last revised 26 October 2024},
+  organization = {Bioconductor},
+  url = {https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf},
+  note = {First edition 17 September 2008}
+}
+
+@incollection{Chen2016,
+  author = {Yunshun Chen and Gordon K. Smyth},
+  title = {It’s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR},
+  booktitle = {Methods in Molecular Biology},
+  volume = {1418},
+  pages = {391--416},
+  year = {2016},
+  publisher = {Springer},
+  doi = {10.1007/978-1-4939-3578-9_19},
+  note = {This book chapter explains the glmQLFit and glmQLFTest functions, which are alternatives to glmFit and glmLRT. They replace the chi-square approximation to the likelihood ratio statistic with a quasi-likelihood F-test, resulting in more conservative and rigorous type I error rate control.}
+}