APAlyzer

A toolkit for APA analysis using RNA-seq data

Bioconductor version: 3.23 · Package version: 1.26.0

Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("APAlyzer")

Maintainer	Ruijia Wang <rjwang.bioinfo@gmail.com>
Author	Ruijia Wang [cre, aut] (ORCID: <https://orcid.org/0000-0002-4211-5207>), Bin Tian [aut], Wei-Chun Chen [aut]
License	LGPL-3 + file LICENSE
URL	https://github.com/RJWANGbioinfo/APAlyzer/
Bug Reports	https://github.com/RJWANGbioinfo/APAlyzer/issues
Downloads rank	259
Source branch	RELEASE_3_23
biocViews	Annotation, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, RNASeq, Sequencing, Software

Dependencies

Depends: R (>= 3.5.0)

Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, rlang, txdbmaker, S4Vectors

Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset, HybridMTest