Package: MAnorm2 1.2.2

MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples

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) <doi:10.1101/gr.262675.120> and Chen et al. (2022) <doi:10.1186/s13059-022-02627-9> for associated statistical details.

Authors:Shiqi Tu [aut, cre]

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MAnorm2/json (API)

# Install 'MAnorm2' in R:

install.packages('MAnorm2', repos = c('https://tushiqi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tushiqi/manorm2/issues

Datasets:

H3K27Ac - ChIP-seq Samples for H3K27Ac in Human Lymphoblastoid Cell Lines

On CRAN:

chip-seq differential-analysis empirical-bayes winsorize-values

5.66 score 33 stars 28 scripts 407 downloads 1 mentions 41 exports 13 dependencies

Last updated from:5fd6bdb1a1. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	150
source / vignettes	OK	213
linux-release	OK	143
macos-release	OK	178
macos-oldrel	OK	196
windows-devel	OK	107
windows-release	OK	103
windows-oldrel	OK	112
wasm-release	OK	96

Exports:aovBioCond bioCond cmbBioCond diffTest diffTest.bioCond distBioCond estimatePriorDf estimatePriorDfRobust estimateSizeFactors estimateVarRatio estParamHyperChIP extendMeanVarCurve fitMeanVarCurve inv.trigamma isSymPosDef MAplot MAplot.bioCond MAplot.default MAplot.diffBioCond mean_var_logwinf normalize normalizeBySizeFactors normBioCond normBioCondBySizeFactors plot.aovBioCond plot.matrix plot.varTestBioCond plotMeanVarCurve plotMVC print.bioCond print.summaryBioCond setMeanVarCurve setPriorDf setPriorDfRobust setPriorDfVarRatio setWeight summary.bioCond util.trigamma varRatio varTestBioCond vstBioCond

Dependencies:cli farver glue labeling lattice lifecycle locfit R6 RColorBrewer rlang scales statmod viridisLite

MAnorm2 for Normalizing and Comparing ChIP-seq Samples

Rendered fromMAnorm2_vignette.Rmdusingknitr::rmarkdown

Last update: 2022-10-31
Started: 2020-01-09

Help page	Topics
Perform a Moderated Analysis of Variance on 'bioCond' Objects	aovBioCond
Create a 'bioCond' Object to Group ChIP-seq Samples	bioCond
Check the Regularity of a Count Table	checkCountTable
Check the Validity of an Index Vector	checkIndex
Combine a Set of 'bioCond' Objects into a Single 'bioCond'	cmbBioCond
Generic Differential Test	diffTest diffTest.bioCond
Quantify the Distance between Each Pair of Samples in a 'bioCond'	distBioCond
Workhorse Function for Estimating Number of Prior Degrees of Freedom	estimateD0
Estimate Number of Prior Degrees of Freedom in a Robust Manner	estimateD0Robust
Assess the Goodness of Fit of Mean-Variance Curves	estimatePriorDf
Assess the Goodness of Fit of Mean-Variance Curves in a Robust Manner	estimatePriorDfRobust
Estimate Size Factors of ChIP-seq Samples	estimateSizeFactors
Estimate Relative Variance Ratio Factors of 'bioCond' Objects	estimateVarRatio
The Parameter Estimation Framework of HyperChIP	estParamHyperChIP
Extend the Application Scope of a Mean-Variance Curve	extendMeanVarCurve
Fit a Mean-Variance Curve	fitMeanVarCurve
ChIP-seq Samples for H3K27Ac in Human Lymphoblastoid Cell Lines	H3K27Ac
Deduce the Sample Mean Signal Intensity	intervalMeans
Sample Variance of Replicated Signal Intensities	intervalVars
Inversion of Trigamma Function	inv.trigamma
Is a Real Matrix Symmetric and Positive Definite?	isSymPosDef
Deduce Pearson Correlation Coefficient between M & A Values	MA.pcc
MAnorm2: a Package for Normalizing and Comparing ChIP-seq Samples	MAnorm2
Generic MA Plotting	MAplot MAplot.default
Create an MA Plot on Two 'bioCond' Objects	MAplot.bioCond
Create an MA Plot on Results of Comparing Two 'bioCond' Objects	MAplot.diffBioCond
Expectation and Variance of Log Winsorized _F_ Distribution	mean_var_logwinf
Fit Mean-Variance Trend by Local Regression	meanVarLocalFit
Parametrically Fit a Mean-Variance Curve	meanVarParaFit
Create a New Unique ID for a Mean-Variance Curve	mvcID.new
Perform MA Normalization on a Set of ChIP-seq Samples	normalize
Normalize ChIP-seq Samples by Their Size Factors	normalizeBySizeFactors
Perform MA Normalization on a Set of 'bioCond' Objects	normBioCond
Normalize 'bioCond' Objects by Their Size Factors	normBioCondBySizeFactors
Deduce MA Normalization Coefficients	normCoef
Plot an 'aovBioCond' Object	plot.aovBioCond
Visualize a Matrix of Numeric Values	plot.matrix
Plot a 'varTestBioCond' Object	plot.varTestBioCond
Plot a Mean-Variance Curve	plotMeanVarCurve
Plot a Mean-Variance Curve on a Single 'bioCond' Object	plotMVC
Print a 'bioCond' Object	print.bioCond
Print a 'summaryBioCond' Object	print.summaryBioCond
Scale a Mean-Variance Curve	scaleMeanVarCurve
Scale a Mean-Variance Curve in a Robust Manner	scaleMeanVarCurveRobust
Set the Mean-Variance Curve of a Set of 'bioCond' Objects	setMeanVarCurve
Set the Number of Prior Degrees of Freedom of Mean-Variance Curves	setPriorDf
The Robust Counterpart of 'setPriorDf'	setPriorDfRobust
Set the Number of Prior Degrees of Freedom and Variance Ratio Factors	setPriorDfVarRatio
Set the Weights of Signal Intensities Contained in a 'bioCond'	setWeight
Summarize a 'bioCond' Object	summary.bioCond
Utility Trigamma Function	util.trigamma
Compare Variance Ratio Factors of Two 'bioCond' Objects	varRatio
Call Hypervariable and Invariant Intervals for a 'bioCond'	varTestBioCond
Apply a Variance-Stabilizing Transformation to a 'bioCond'	vstBioCond

Package: MAnorm2 1.2.2

MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples

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