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 (3.22)
This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy. It provides estimates for each gene within each sample.
Author: Ji-Ping Wang [aut, cre]
Maintainer: Ji-Ping Wang <jzwang at northwestern.edu>
citation("DegNorm")):
Installation
To install this package, start R (version "4.5") 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 | 1.19.1 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 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_1.19.1.tar.gz |
| Windows Binary (x86_64) | DegNorm_1.19.1.zip |
| macOS Binary (x86_64) | DegNorm_1.19.1.tgz |
| macOS Binary (arm64) | DegNorm_1.19.1.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 |