{"repo":"epigen/dea_seurat","free":true,"listed":false,"github":"https://github.com/epigen/dea_seurat","clone":"git clone https://github.com/epigen/dea_seurat.git","description":"A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.","language":"R","stars":56,"topics":["bioinformatics","biomedical-data-science","differential-expression-analysis","scrna-seq","single-cell","snakemake","snrna-seq","visualization","workflow","volcano-plot"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis & Visualization Workflow A Snakemake 8 workflow for performing differential expression analyses (DEA) of processed (multimodal) scRNA-seq data powered by the R package Seurat's functions FindMarkers and FindAllMarkers. [!NOTE] This workflow adheres to the module specifications of MrBiomics, an effort to augment research by modularizing (biomedical) data science. For more details, instructions, and modules check out the project's repository. ⭐️ Star and share modules you find valuable 📤 - help others discover them, and guide our future work! [!IMPORTANT] If you use this workflow in a publication, please don't forget to give credit to the authors by citing it using this DOI 10.5281/zenodo.10689139. 🖋️ Authors - Stephan Reichl - Christoph Bock 💿 Software This project wouldn't be possible without the following software and their dependencies: Software Reference (DOI) :------------: :-----------------------------------------------: data.table https://r-datatable.com EnhancedVolcano https://doi.org/10.18129/B9.bioc.EnhancedVolcano future https://doi.org/10.32614/RJ-2021-048 ggplot2 https://ggplot2.tidyverse.org/ pheatmap https://cran.r-project.org/package=pheatmap Seurat https://doi.org/10.1016/j.cell.2021.04.048 Snakemake https://doi.org/10.12688/f1000research.29032.2 🔬 Methods This is a template for the Methods section of a scientific publication and is intended to serve as a starting point. Only retain p","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/dea_seurat/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}