Linnorm
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see Linnorm.
Linear model and normality based normalization and transformation method (Linnorm)
Bioconductor version: 3.10
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("Linnorm")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Network, Normalization, PeakDetection, RNASeq, Sequencing, SingleCell, Software, Transcription |
| Version | 2.10.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 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 |
| System Requirements | |
| URL | https://doi.org/10.1093/nar/gkx828 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments, testthat |
| 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_2.10.0.tar.gz |
| Windows Binary | Linnorm_2.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | Linnorm_2.10.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |