Package: mosaics 2.43.0

Dongjun Chung

mosaics: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.

Authors:Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles

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mosaics.pdf |mosaics.html✨
mosaics/json (API)
NEWS

# Install 'mosaics' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:mosaics-2.43.0(bioc 3.20)mosaics-2.42.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

31 exports 0.82 score 44 dependencies

Last updated 2 months agofrom:9ffe768a6f

Exports:adjustBoundary bdBin chrID constructBins conv_1S conv_2S coord empFDR estimates export extractReads filterPeak findSummit gcContent generateWig input mappability mosaicsFit mosaicsFitHMM mosaicsPeak mosaicsPeakHMM mosaicsRunAll plot postProb print read readBins readCoverage seqDepth show tagCount

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice MASS Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp Rhtslib Rsamtools S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

MOSAiCS

Rendered frommosaics-example.Rnwusingutils::Sweaveon Jun 20 2024.

Last update: 2016-08-11
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)	mosaics-package mosaics
Adjust boundaries of peak regions	adjustBoundary adjustBoundary,MosaicsPeak-method
Class "BinData"	BinData-class chrID chrID,BinData-method coord coord,BinData-method gcContent gcContent,BinData-method input input,BinData-method mappability mappability,BinData-method plot,BinData,missing-method print,BinData-method seqDepth seqDepth,BinData-method show,BinData-method tagCount tagCount,BinData-method
Construct bin-level ChIP-sep data from an aligned read file	constructBins
Extract estimates of the fitted MOSAiCS model	estimates estimates,MosaicsFit-method
Export peak calling results to text files	export export,MosaicsPeak-method
Load read-level data and extract reads corresponding to each peak region	extractReads extractReads,MosaicsPeak-method
Filter out potentially false positive peaks	filterPeak filterPeak,MosaicsPeak-method
Find a summit for each peak region	findSummit findSummit,MosaicsPeak-method
Construct wiggle files from an aligned ChIP-sep read file	generateWig
Fit MOSAiCS model	mosaicsFit mosaicsFit,BinData-method
Class "MosaicsFit"	MosaicsFit-class plot,MosaicsFit,ANY-method print,MosaicsFit-method seqDepth,MosaicsFit-method show,MosaicsFit-method
Class "MosaicsFitEst"	MosaicsFitEst-class
Fit MOSAiCS-HMM model	mosaicsFitHMM mosaicsFitHMM,MosaicsFit-method
Class "MosaicsFitParam"	MosaicsFitParam-class
Class "MosaicsHMM"	estimates,MosaicsHMM-method MosaicsHMM-class plot,MosaicsHMM,missing-method print,MosaicsHMM-method seqDepth,MosaicsHMM-method show,MosaicsHMM-method
Call peaks using fitted MOSAiCS model	mosaicsPeak mosaicsPeak,MosaicsFit-method
Class "MosaicsPeak"	bdBin bdBin,MosaicsPeak-method empFDR empFDR,MosaicsPeak-method MosaicsPeak-class plot,MosaicsPeak,missing-method postProb postProb,MosaicsPeak-method print,MosaicsPeak-method read read,MosaicsPeak-method readCoverage readCoverage,MosaicsPeak-method seqDepth,MosaicsPeak-method show,MosaicsPeak-method
Call broad peaks using fitted MOSAiCS-HMM model	mosaicsPeakHMM mosaicsPeakHMM,MosaicsHMM-method
Class "MosaicsPeakParam"	MosaicsPeakParam-class
Analyze ChIP-seq data using the MOSAiCS framework	mosaicsRunAll
Import bin-level ChIP-sep data	readBins
Class "TagData"	TagData-class