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 (3.20)
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 "4.4") and enter:
if (!require("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")
DegNorm | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Alignment, BatchEffect, Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, QualityControl, RNASeq, Sequencing, Software |
Version | 1.15.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
License | LGPL (>= 3) |
Depends | R (>= 4.0.0), methods |
Imports | Rcpp (>= 1.0.2), GenomicFeatures, txdbmaker, 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_1.15.0.tar.gz |
Windows Binary | DegNorm_1.15.0.zip |
macOS Binary (x86_64) | DegNorm_1.15.0.tgz |
macOS Binary (arm64) | DegNorm_1.15.0.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 |