APAlyzer
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see APAlyzer.
A toolkit for APA analysis using RNA-seq data
Bioconductor version: 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 | ||
| 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 | |
| Links To Me | |
| 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 |