# Identify Differentially Expressed Genes from RNA-seq data

## Documentation for package ‘DEGseq’ version 1.2.2

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

DEGexp | DEGexp: Identifying Differentially Expressed Genes from gene expression data
DEGexp2 | DEGexp2: Identifying Differentially Expressed Genes from gene expression data
DEGseq | DEGseq: Identify Differentially Expressed Genes from RNA-seq data
DEGseq.aln | DEGseq.aln: Identify Differentially Expressed Genes from RNA-seq data (deal with the objects of class AlignedRead)
GeneExpExample1000 | GeneExpExample1000
GeneExpExample5000 | GeneExpExample5000
getGeneExp | getGeneExp: Count the number of reads and calculate the RPKM for each gene
getGeneExp.aln | getGeneExp.aln: Count the number of reads and calculate the RPKM for each gene (deal with the objects of class AlignedRead)
kidneyChr21.bed | kidneyChr21.bed
kidneyChr21Bowtie | kidneyChr21Bowtie
liverChr21.bed | liverChr21.bed
liverChr21Bowtie | liverChr21Bowtie
readGeneExp | readGeneExp: read gene expression values to a matrix
refFlatChr21 | refFlatChr21
samWrapper | samWrapper: A Wrapper (with some modification) of the functions in the package samr to identify differentially expressed genes for the RNA-seq data from two groups of paired or unpaired samples.