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APAlyzer

This is the development version of APAlyzer; for the stable release version, see APAlyzer.

A toolkit for APA analysis using RNA-seq data


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
Links To Me
Build Report Build Report

Package Archives

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

Source Package APAlyzer_1.17.0.tar.gz
Windows Binary APAlyzer_1.17.0.zip
macOS Binary (x86_64) APAlyzer_1.17.0.tgz
macOS Binary (arm64) APAlyzer_1.17.0.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