{"repo":"epigen/mixscape_seurat","free":true,"listed":false,"github":"https://github.com/epigen/mixscape_seurat","clone":"git clone https://github.com/epigen/mixscape_seurat.git","description":"A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.","language":"R","stars":56,"topics":["bioinformatics","biomedical-data-science","perturbation-analysis","sccrispr-seq","scrna-seq","single-cell","snakemake","snrna-seq","visualization","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"scCRISPR-seq Perturbation Analysis Workflow using Seurat's Mixscape A Snakemake 8 workflow for performing perturbation analyses of pooled (multimodal) CRISPR screens with scRNA-seq read-out (scCRISPR-seq, CROP-seq, Perturb-seq) powered by the R package Seurat's method Mixscape. [!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.8424761. Authors - Stephan Reichl - Christoph Bock 💿 Software This project wouldn't be possible without the following software and it's dependencies: Software Reference (DOI) :------------: :-----------------------------------------------: data.table https://r-datatable.com ggplot2 https://ggplot2.tidyverse.org/ Mixscape https://doi.org/10.1038/s41588-021-00778-2 mixtools https://CRAN.R-project.org/package=mixtools patchwork https://CRAN.R-project.org/package=patchwork 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 t","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/mixscape_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."}