Hallacli2022Cell

Bioinformatics code repository for Hallacli et al. Cell 2022

./src/main.sh

The primary bash script includes multiple steps of the pipeline:

• process each sample (e.g. QC, mapping, and gene expression quantification), see _RNAseq.lite.sh
• merge all samples to generate gene expression matrix,
• perform sample level QC / outlier detection, see _normQC.R
• DE analysis, see _DE.R and _DE2.R

./src/main.R

The R script to concatenate multi-timepoint consecutive analysis result together.