R

RNA-Seq

a fast xenograft read sorter based on space-efficient k-mer hashing, efficiently paralellized, written in jit-compiled Python using numba. Since 2.1.0, xengsort supports also WGBS data in addition to RNA-seq, whole genome and exome data.

Splicing analysis: Extract from mapped RNA-Seq-reads information on intron removal-order for exons genome-wide, and estimate their PSI values (percent-spliced-in) and PIR values (percent-intron-retention) of their flanking introns.

StCsm next-generation sequencing data processing Nextflow pipeline.

StCsm sequencing data analysis in R programming language.

DEGs analysis of bulk RNA-seq data using edgeR

Allows table cleaning containing RNAseq data (number of counts per genes).