APAlyzer

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see APAlyzer.

All versions

3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10

A toolkit for APA analysis using RNA-seq data

Bioconductor version: Release (3.23)

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

Author: Ruijia Wang [cre, aut] ORCID: 0000-0002-4211-5207 , Bin Tian [aut], Wei-Chun Chen [aut]

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

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

Ruijia Wang, Bin Tian, Wei-Chun Chen. APAlyzer: A toolkit for APA analysis using RNA-seq data. doi:10.18129/B9.bioc.APAlyzer, R package version 1.26.0, https://bioconductor.org/packages/APAlyzer.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, RNASeq, Sequencing, Software
Version	1.26.0
In Bioconductor since	BioC 3.10 (R-3.6) (7 years)
License	LGPL-3 + file LICENSE
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
System Requirements
URL	https://github.com/RJWANGbioinfo/APAlyzer/
Bug Reports	https://github.com/RJWANGbioinfo/APAlyzer/issues

Suggests	knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset, HybridMTest
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	APAlyzer_1.26.0.tar.gz
Windows Binary (x86_64)	APAlyzer_1.26.0.zip
macOS Binary (big-sur-x86_64)	APAlyzer_1.26.0.tgz
macOS Binary (sonoma-arm64)	APAlyzer_1.26.0.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