https://github.com/batoolmm/scrna
This is an exercise for scRNA
https://github.com/batoolmm/scrna
Last synced: 17 days ago
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This is an exercise for scRNA
- Host: GitHub
- URL: https://github.com/batoolmm/scrna
- Owner: BatoolMM
- Created: 2022-01-22T13:22:02.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2022-01-22T13:27:27.000Z (about 4 years ago)
- Last Synced: 2025-09-09T13:59:25.414Z (5 months ago)
- Language: HTML
- Size: 6.26 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# scRNA-seq Analysis Workshop
This workshop is imported from [David Cook on 2020](https://github.com/dpcook/scrna_seq_workshop_2020).
All data and notebook for my 2020 scRNA-seq analysis workshop. This workshop will contain a fairly straight forward processing and exploratory data analysis pipeline for the 10x Genomics 8k PBMC data set.
**Download/clone the entire repository to download all required data and maintain the folder structure referrenced within the R scripts**
HTML documents in the main directory contain knitted RMD files of the analysis with a decent amount of documentation.
The notebooks/ subfolder contains the R scripts themselves. Begin with the package_installation.R script, followed by 01_processing, and then 02_downstream_analysis.
The data/ subfolder contains the CellRanger output provided by 10x Genonmics, along with some MSigDB gene set lists.
**I could not fit the matrix.mtx file from CellRanger into this repo. Please download the file from https://drive.google.com/drive/folders/1szqYwvJvp8gV0SOv_VQJNDAh4wQyhlMk?usp=sharing and place it in data/filtered_gene_bc_matrices_8kpbmc/GRCh38/**