DegNorm

DOI: 10.18129/B9.bioc.DegNorm  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see DegNorm.

DegNorm: degradation normalization for RNA-seq data

Bioconductor version: 3.17

This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy.

Author: Bin Xiong and Ji-Ping Wang

Maintainer: Ji-Ping Wang <jzwang at northwestern.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DegNorm")

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("DegNorm")

 

HTML	R Script	DegNorm
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, BatchEffect, Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, QualityControl, RNASeq, Sequencing, Software
Version	1.10.1
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	LGPL (>= 3)
Depends	R (>= 4.0.0), methods
Imports	Rcpp (>= 1.0.2), GenomicFeatures, parallel, foreach, S4Vectors, doParallel, Rsamtools(>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils, viridis
LinkingTo	Rcpp, RcppArmadillo, S4Vectors, IRanges
Suggests	knitr, rmarkdown, formatR
SystemRequirements
Enhances
URL
BugReports	https://github.com/jipingw/DegNorm/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	DegNorm_1.10.1.tar.gz
Windows Binary	DegNorm_1.10.1.zip
macOS Binary (x86_64)	DegNorm_1.10.1.tgz
macOS Binary (arm64)	DegNorm_1.10.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DegNorm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DegNorm
Bioc Package Browser	https://code.bioconductor.org/browse/DegNorm/
Package Short Url	https://bioconductor.org/packages/DegNorm/
Package Downloads Report	Download Stats