APABox                  APABox, APA RED Box plotting
APAVolcano              APAVolcano, APA Volcano plotting
APAdiff                 APAdiff, calculate delta relative expression
                        (RED) and statistics significance between two
                        sample groups
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
download_testbam        download_testbam, download bam files of mouse
                        testis and heart
