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Linnorm

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

Bioconductor version: 3.24 · Package version: 2.37.0

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.

Installation

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

BiocManager::install("Linnorm")

Details

MaintainerShun Hang Yip <shunyip@bu.edu>
AuthorShun Hang Yip <shunyip@bu.edu>
LicenseMIT + file LICENSE
URLhttps://doi.org/10.1093/nar/gkx828
Downloads rank686
Source branchdevel
biocViewsBatchEffect, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Network, Normalization, PeakDetection, RNASeq, Sequencing, SingleCell, Software, Transcription

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageLinnorm_2.37.0.tar.gz
Windows binary (x86_64)Linnorm_2.37.0.zip
macOS binary (arm64)Linnorm_2.37.0.tgz
macOS binary (x86_64)Linnorm_2.37.0.tgz
Dependencies

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

LinkingTo: Rcpp, RcppArmadillo

Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats

Reverse dependencies

Imports Me (1): mnem