Linnorm

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see Linnorm.

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

Bioconductor version: 3.21

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 "4.5") 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 2.32.0

In Bioconductor since BioC 3.3 (R-3.3) (9.5 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 SCdeconR

Links To Me

Build Report Build Report

Package Archives

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

Source Package Linnorm_2.32.0.tar.gz

Windows Binary (x86_64) Linnorm_2.32.0.zip

macOS Binary (x86_64) Linnorm_2.32.0.tgz

macOS Binary (arm64) Linnorm_2.32.0.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/

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