APAlyzer

DOI: 10.18129/B9.bioc.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 (3.11)

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

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

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

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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 1.1.2
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License LGPL-3
Depends R (>= 3.5.0)
Imports GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, ensembldb, VariantAnnotation, dplyr, tidyr, repmis
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, Rsamtools, testthat
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_1.1.2.tar.gz
Windows Binary APAlyzer_1.1.2.zip
Mac OS X 10.11 (El Capitan)
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

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