{"repo":"epigen/scrnaseq_processing_seurat","free":true,"listed":false,"github":"https://github.com/epigen/scrnaseq_processing_seurat","clone":"git clone https://github.com/epigen/scrnaseq_processing_seurat.git","description":"A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.","language":"R","stars":60,"topics":["bioinformatics","workflow","snakemake","scrna-seq","biomedical-data-science","cite-seq","sccrispr-seq","10xgenomics","snrna-seq","single-cell"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Single-cell RNA sequencing (scRNA-seq) Data Processing & Visualization Workflow A Snakemake 8 workflow for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX file format powered by the R package Seurat. [!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.10679327. 🖋️ Authors - Stephan Reichl - Christoph Bock 💿 Software This project wouldn't be possible without the following software and their dependencies. Software Reference (DOI) :------------: :-----------------------------------------------: inspectdf https://github.com/alastairrushworth/inspectdf/ data.table https://r-datatable.com SCTransform https://doi.org/10.1186/s13059-019-1874-1 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 paragraphs relevant to your analysis. References [ref] to the respective publications are curated in the software table abov","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/scrnaseq_processing_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."}