alaaalatif / sc_rna_seq

A repository containing usable code for processing and analysis of single-cell RNAseq data

sc_rna_seq

A repository containing usable code for processing and analysis of single-cell RNAseq data.

Pre-requisites

Usage of this code expects familiarity with the following:

• Linux/Unix command-line system
• R programming language
• computational single-cell RNA sequencing analysis

As of now, the constituent scripts (src/quality_control.R) expects the user to have completed pre-processing of the raw FASTQ files using cellranger and thus, to have generated files corresponding to the:

• filtered cell-by-gene count data
• raw count data
• cluster assignments of each cell generated by cellranger

Installation

Prior to using the code in this repository, the user is expected to have the following installed in their computing environment:

• R programming language
• the following R packages
  • jsonlite
  • ggplot2
  • tidyverse
  • Matrix
  • Seurat
  • SeuratObject
  • scales
  • harmony
  • cowplot
  • purrr
  • plyr
  • patchwork
  • SoupX
  • DoubletFinder

Usage

• open the configuration file cfg/quality_control.json
• specify all the required parameters
• save the configuration file
• run the QC script

Rscript src/quality_control.R

Authors

Al Latif