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DegNorm

DegNorm: degradation normalization for RNA-seq data


Bioconductor version: Release (3.18)

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 "4.3") 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")
DegNorm HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, BatchEffect, Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, QualityControl, RNASeq, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
System Requirements
URL
Bug Reports https://github.com/jipingw/DegNorm/issues
See More
Suggests knitr, rmarkdown, formatR
Linking To Rcpp, RcppArmadillo, S4Vectors, IRanges
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 DegNorm_1.12.0.tar.gz
Windows Binary DegNorm_1.12.0.zip (64-bit only)
macOS Binary (x86_64) DegNorm_1.12.0.tgz
macOS Binary (arm64) DegNorm_1.12.0.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