APAlyzer

DOI: 10.18129/B9.bioc.APAlyzer    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see APAlyzer.

A toolkit for APA analysis using RNA-seq data

Bioconductor version: 3.13

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

Author: Ruijia Wang [cre, aut] , Bin Tian [aut], Chuwei Zhong [aut]

Maintainer: Ruijia Wang <rjwang.bioinfo at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("APAlyzer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("APAlyzer")

 

HTML	R Script	APAlyzer: toolkit for RNA-seq APA analysis
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, RNASeq, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	LGPL-3
Depends	R (>= 3.5.0)
Imports	GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, ensembldb, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset
SystemRequirements
Enhances
URL	https://github.com/RJWANGbioinfo/APAlyzer/
BugReports	https://github.com/RJWANGbioinfo/APAlyzer/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	APAlyzer_1.6.0.tar.gz
Windows Binary	APAlyzer_1.6.0.zip
macOS 10.13 (High Sierra)	APAlyzer_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/APAlyzer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/APAlyzer
Package Short Url	https://bioconductor.org/packages/APAlyzer/
Package Downloads Report	Download Stats