# A toolkit for APA analysis using RNA-seq data

## Documentation for package ‘APAlyzer’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

APABox | APABox, APA RED Box plotting
APAdiff | APAdiff, calculate delta relative expression (RED) and statistics significance between two sample groups
APAVolcano | APAVolcano, APA Volcano plotting
download_testbam | download_testbam, download bam files of mouse testis and heart
GENEXP_CDS | GENEXP_CDS, count reads mapped to CDS regions and calculate TPM for coding gene
PAS2GEF | PAS2GEF, build reference regions for 3'UTR PASs
PASEXP_3UTR | PASEXP_3UTR, calculate relative expression of aUTR and cUTR regions
PASEXP_IPA | PASEXP_IPA, calculate relative expression of IPA regions
REF3UTR | REF3UTR, build reference regions for 3'UTR PASs
REF4PAS | REF4PAS, build reference regions for 3'UTR and Intronic PAS using dataframe formated input
REFCDS | REFCDS, build reference regions for CDS of protein coding genes
ThreeMostPairBam | ThreeMostPairBam, extract 3 prime most alignment of a paired-end bam file