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APAlyzer

A toolkit for APA analysis using RNA-seq data

Bioconductor version: Release (3.17)

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

Author: Ruijia Wang [cre, aut] , Bin Tian [aut], Wei-Chun Chen [aut]

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

Citation (from within R, enter citation("APAlyzer")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("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")
APAlyzer: toolkit for RNA-seq APA analysis HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, RNASeq, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License LGPL-3
Depends R (>= 3.5.0)
Imports GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, HybridMTest
Linking To
Suggests knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset
System Requirements
Enhances
URL https://github.com/RJWANGbioinfo/APAlyzer/
Bug Reports https://github.com/RJWANGbioinfo/APAlyzer/issues
See More
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_1.14.0.tar.gz
Windows Binary APAlyzer_1.14.0.zip
macOS Binary (x86_64) APAlyzer_1.14.0.tgz
macOS Binary (arm64) APAlyzer_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/APAlyzer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/APAlyzer
Bioc Package Browser https://code.bioconductor.org/browse/APAlyzer/
Package Short Url https://bioconductor.org/packages/APAlyzer/
Package Downloads Report Download Stats