Linnorm

This is the released version of Linnorm; for the devel version, see Linnorm.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Linear model and normality based normalization and transformation method (Linnorm)

Bioconductor version: Release (3.23)

Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.

Author: Shun Hang Yip <shunyip at bu.edu>

Maintainer: Shun Hang Yip <shunyip at bu.edu>

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

Shun Hang Yip. Linnorm: Linear model and normality based normalization and transformation method (Linnorm). doi:10.18129/B9.bioc.Linnorm, R package version 2.36.0, https://bioconductor.org/packages/Linnorm.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("Linnorm")

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("Linnorm")

Linnorm User Manual	PDF	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BatchEffect, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Network, Normalization, PeakDetection, RNASeq, Sequencing, SingleCell, Software, Transcription
Version	2.36.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels
System Requirements
URL	https://doi.org/10.1093/nar/gkx828

Suggests	BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats
Linking To	Rcpp, RcppArmadillo
Enhances
Depends On Me
Imports Me	mnem
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Linnorm_2.36.0.tar.gz
Windows Binary (x86_64)	Linnorm_2.36.0.zip
macOS Binary (big-sur-x86_64)	Linnorm_2.36.0.tgz
macOS Binary (sonoma-arm64)	Linnorm_2.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Linnorm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Linnorm
Package Short Url	https://bioconductor.org/packages/Linnorm/
Package Downloads Report	Download Stats