APAlyzer

A toolkit for APA analysis using RNA-seq data


Bioconductor version: Release (3.19)

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 "4.4") 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 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (5 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
System Requirements
URL https://github.com/RJWANGbioinfo/APAlyzer/
Bug Reports https://github.com/RJWANGbioinfo/APAlyzer/issues
See More
Suggests knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package APAlyzer_1.18.0.tar.gz
Windows Binary (x86_64) APAlyzer_1.18.0.zip
macOS Binary (x86_64) APAlyzer_1.18.0.tgz
macOS Binary (arm64) APAlyzer_1.18.0.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