Linnorm

DOI: 10.18129/B9.bioc.Linnorm    

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

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

Bioconductor version: Development (3.11)

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>, Panwen Wang <pwwang at pwwang.com>, Jean-Pierre Kocher <Kocher.JeanPierre at mayo.edu>, Pak Chung Sham <pcsham at hku.hk>, Junwen Wang <junwen at uw.edu>

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

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

Installation

To install this package, start R (version "4.0") and enter:

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

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

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")

 

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

Details

biocViews BatchEffect, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Network, Normalization, PeakDetection, RNASeq, Sequencing, SingleCell, Software, Transcription
Version 2.11.0
In Bioconductor since BioC 3.3 (R-3.3) (3.5 years)
License MIT + file LICENSE
Depends R (>= 3.4)
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
LinkingTo Rcpp, RcppArmadillo
Suggests BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments, testthat
SystemRequirements
Enhances
URL https://doi.org/10.1093/nar/gkx828
Depends On Me
Imports Me mnem
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package Linnorm_2.11.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) Linnorm_2.11.0.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

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