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      Single Cell RNA-Seq Analysis

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Introduction and Lectures
Intro to the Workshop and Core
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Prerequisites
CLI
R
Data Reduction
Files and Filetypes
Project setup
Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
Part 1- Create object
Part 2- Filtering
Part 3- Normalization and scaling
Part 4- Dimensionality reduction
Part 5- Clustering and cell type
Part 6- Enrichment and DE
Part 7- Doublet detection
Part 8- Integration

Slurm script for cellranger counts

Cellranger counts

Bash script (loop) for cellranger counts

Cellranger counts