DegNorm

DOI: 10.18129/B9.bioc.DegNorm    

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

DegNorm: degradation normalization for RNA-seq data

Bioconductor version: Development (3.13)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

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

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

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 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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_1.1.0.tar.gz
Windows Binary DegNorm_1.1.0.zip
macOS 10.13 (High Sierra) DegNorm_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DegNorm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DegNorm
Package Short Url https://bioconductor.org/packages/DegNorm/
Package Downloads Report Download Stats

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