Bioinformatics Data Analysis Pipeline- RNA-Seq

EdgeR

Differential expression analysis using bulk RNA-seq data
Reference: PMID: 19910308
Contact: Qin Ma
DESeq2

Differential expression analysis using bulk RNA-seq data.
Reference: PMID: 25516281
Contact: Qin Ma
Limma

Differential expression analysis using bulk RNA-seq and microarray data.
Reference: PMID: 25605792
Contact: Qin Ma
RSeQC

RNAseq quality control package.
Reference: PMID:22743226
Contact: Qin Ma
JunctionSeq

Bioconductor package for detection and visualization of differential usage of exons and splice junctions in High-Throughput, Next-Generation RNA-Seq datasets.
Reference: PMID: 27257077
Contact: Qin Ma
CIBERSORT

A deconvolution-based method thats estimates each immune cell type's relative proportion from a gene expression profile (GEP).
Reference: PMID: 29344893
Contact: Qin Ma