.build_pileupExon       Core helper to build exon-only pileup
TOY_mrna_mat            Toy mRNA-seq-like dataset for RNAshapeQC
                        (matrix input)
TOY_mrna_se             Toy mRNA-seq-like dataset for RNAshapeQC (SE
                        input)
TOY_total_mat           Toy total RNA-seq-like dataset for RNAshapeQC
                        (matrix input)
TOY_total_se            Toy total RNA-seq-like dataset for RNAshapeQC
                        (SE input)
combine_vecObj          Combine vectors as a matrix from objects
compute_DIIwt           Core helper to compute a degraded/intact index
                        using gene weight
compute_DR              Core helper to compute decay rate
compute_MCD             Core helper to compute a mean coverage depth
compute_SOI             Core helper to compute a suboptimal/optimal
                        index
compute_wCV             Core helper to compute a window coefficient of
                        variation
construct_pileup        Construct a per-gene pileup from BAM files (for
                        single-study or multi-study)
extract_RData           Extract an object from .RData
filter_lowExpGenes      Filter low expressed genes
gen_DR                  Get a decay rate for genes and samples (for a
                        single gene)
gen_MCD                 Get a mean coverage depth for genes and samples
                        (for a single gene)
gen_wCV                 Get a window coefficient of variation for genes
                        and samples (for a single gene)
get_DIIhc               Get a degraded/intact index for samples using
                        hierarchical clustering
get_DIIwt               Get a degraded/intact index for samples using
                        gene weight
get_DR                  Get a decay rate for genes and samples (for a
                        genelist)
get_MCD                 Get a mean coverage depth for genes and samples
                        (for a genelist)
get_SOI                 Get a suboptimal/optimal index for samples
get_pileupExon          Get a focused pileup of exon location (for
                        single-study)
get_wCV                 Get a window coefficient of variation for genes
                        and samples (for a genelist)
plot_DIIwt              Plot degraded/intact index outputs
plot_GBC                Plot gene body coverage
plot_GBCos              Plot gene body coverage with optimal samples
plot_SOI                Plot suboptimal/optimal index outputs
