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MAnorm2
View on CRAN: Click
here
Download and install MAnorm2 package within the R console
Install from CRAN:
install.packages("MAnorm2")
Install from Github:
library("remotes")
install_github("cran/MAnorm2")
Install by package version:
library("remotes")
install_version("MAnorm2", "1.2.2")
Attach the package and use:
library("MAnorm2")
Maintained by
Shiqi Tu
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
10.32614/CRAN.package.MAnorm2 . https://github.com/tushiqi/MAnorm2/issues . https://github.com/tushiqi/MAnorm2 . MAnorm2 citation info . MAnorm2 results . MAnorm2.pdf . MAnorm2 for Normalizing and Comparing ChIP-seq Samples . MAnorm2_1.2.2.tar.gz . MAnorm2_1.2.2.zip . MAnorm2_1.2.2.zip . MAnorm2_1.2.2.zip . MAnorm2_1.2.2.tgz . MAnorm2_1.2.2.tgz . MAnorm2_1.2.2.tgz . MAnorm2_1.2.2.tgz . MAnorm2 archive . https://CRAN.R-project.org/package=MAnorm2 .
First Published: 2021-09-13
Latest Update: 2022-10-28
Description:
Chromatin immunoprecipitation followed by high-throughput
sequencing (ChIP-seq) is the premier technology for profiling genome-wide
localization of chromatin-binding proteins, including transcription
factors and histones with various modifications.
This package provides a robust method for normalizing ChIP-seq
signals across individual samples or groups of samples. It also designs
a self-contained system of statistical models for calling differential
ChIP-seq signals between two or more biological conditions as well as
for calling hypervariable ChIP-seq signals across samples. Refer to
Tu et al. (2021) and
Chen et al. (2022)
for associated statistical details.
How to cite:
Shiqi Tu (2021). MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples. R package version 1.2.2, https://cran.r-project.org/web/packages/MAnorm2. Accessed 01 May. 2025.
Other packages that cited MAnorm2 R package
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Other R packages that MAnorm2 depends,
imports, suggests or enhances
Complete documentation for MAnorm2
Functions, R codes and Examples using
the MAnorm2 R package
Some associated functions: H3K27Ac . MA.pcc . MAnorm2 . MAplot.bioCond . MAplot.diffBioCond . MAplot . aovBioCond . bioCond . checkCountTable . checkIndex . cmbBioCond . diffTest . distBioCond . estParamHyperChIP . estimateD0 . estimateD0Robust . estimatePriorDf . estimatePriorDfRobust . estimateSizeFactors . estimateVarRatio . extendMeanVarCurve . fitMeanVarCurve . intervalMeans . intervalVars . inv.trigamma . isSymPosDef . meanVarLocalFit . meanVarParaFit . mean_var_logwinf . mvcID.new . normBioCond . normBioCondBySizeFactors . normCoef . normalize . normalizeBySizeFactors . plot.aovBioCond . plot.matrix . plot.varTestBioCond . plotMVC . plotMeanVarCurve . print.bioCond . print.summaryBioCond . scaleMeanVarCurve . scaleMeanVarCurveRobust . setMeanVarCurve . setPriorDf . setPriorDfRobust . setPriorDfVarRatio . setWeight . summary.bioCond . util.trigamma . varRatio . varTestBioCond . vstBioCond .
Some associated R codes: MAnorm2.R . MAnorm2_ops.R . VST.R . bioCond.R . diffTest.R . fitMeanVarCurve.R . meanVarCurve.R . normalize.R . robustMeanVarCurve.R . show.R . util.R . Full MAnorm2 package functions and examples
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