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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 (3.19)

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")):

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("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

Details

biocViews BatchEffect, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Network, Normalization, PeakDetection, RNASeq, Sequencing, SingleCell, Software, Transcription
Version 2.27.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
See More
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

Package Archives

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

Source Package Linnorm_2.27.0.tar.gz
Windows Binary Linnorm_2.27.0.zip (64-bit only)
macOS Binary (x86_64) Linnorm_2.27.0.tgz
macOS Binary (arm64) Linnorm_2.27.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Linnorm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Linnorm
Bioc Package Browser https://code.bioconductor.org/browse/Linnorm/
Package Short Url https://bioconductor.org/packages/Linnorm/
Package Downloads Report Download Stats