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

Share:

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.

Author
Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles
Date of publication
None
Maintainer
Dongjun Chung <dongjun.chung@gmail.com>
License
GPL (>= 2)
Version
2.12.0
URLs

View on Bioconductor

Man pages

adjustBoundary
Adjust boundaries of peak regions
BinData-class
Class "BinData"
constructBins
Construct bin-level ChIP-sep data from an aligned read file
estimates
Extract estimates of the fitted MOSAiCS model
export
Export peak calling results to text files
extractReads
Load read-level data and extract reads corresponding to each...
findSummit
Find a summit for each peak region
fllterPeak
Filter out potentially false positive peaks
generateWig
Construct wiggle files from an aligned ChIP-sep read file
mosaicsFit
Fit MOSAiCS model
MosaicsFit-class
Class "MosaicsFit"
MosaicsFitEst-class
Class "MosaicsFitEst"
mosaicsFitHMM
Fit MOSAiCS-HMM model
MosaicsFitParam-class
Class "MosaicsFitParam"
MosaicsHMM-class
Class "MosaicsHMM"
mosaics-internal
Internal mosaics objects
mosaics-package
MOSAiCS (MOdel-based one and two Sample Analysis and...
mosaicsPeak
Call peaks using fitted MOSAiCS model
MosaicsPeak-class
Class "MosaicsPeak"
mosaicsPeakHMM
Call broad peaks using fitted MOSAiCS-HMM model
MosaicsPeakParam-class
Class "MosaicsPeakParam"
mosaicsRunAll
Analyze ChIP-seq data using the MOSAiCS framework
readBins
Import bin-level ChIP-sep data
TagData-class
Class "TagData"

Files in this package

mosaics/DESCRIPTION
mosaics/NAMESPACE
mosaics/NEWS
mosaics/R
mosaics/R/AllClasses.R
mosaics/R/AllGenerics.R
mosaics/R/adjustBoundary.R
mosaics/R/base_adapGridMosaicsZ0_IO.R
mosaics/R/base_adapGridMosaicsZ0_OS.R
mosaics/R/base_adapGridMosaicsZ0_TS.R
mosaics/R/base_annotateHMM.R
mosaics/R/base_annotatePeak.R
mosaics/R/base_calcModelBIC.R
mosaics/R/base_calcPN.R
mosaics/R/base_calcYbdAll.R
mosaics/R/base_computeStat.R
mosaics/R/base_constructExtRead.R
mosaics/R/base_convolution_1S_cpp.R
mosaics/R/base_convolution_2S_cpp.R
mosaics/R/base_cpp_call.R
mosaics/R/base_export.R
mosaics/R/base_extractPostProb.R
mosaics/R/base_fitHMM.R
mosaics/R/base_getParamZ0.R
mosaics/R/base_getPi0.R
mosaics/R/base_loadReadData.R
mosaics/R/base_logLik.R
mosaics/R/base_margDist_1S.R
mosaics/R/base_margDist_2S.R
mosaics/R/base_mosaicsZ0.R
mosaics/R/base_mosaicsZ1_1S.R
mosaics/R/base_mosaicsZ1_2S.R
mosaics/R/base_peakCall.R
mosaics/R/base_plotGOF.R
mosaics/R/base_plotGOFHMM.R
mosaics/R/base_reportSummary.R
mosaics/R/base_rlmFit_IO.R
mosaics/R/base_rlmFit_OS.R
mosaics/R/base_rlmFit_TS.R
mosaics/R/base_trimExtend.R
mosaics/R/constructBins.R
mosaics/R/extractReads.R
mosaics/R/filterPeak.R
mosaics/R/findSummit.R
mosaics/R/generateWig.R
mosaics/R/methods_BinData.R
mosaics/R/methods_MosaicsFit.R
mosaics/R/methods_MosaicsHMM.R
mosaics/R/methods_MosaicsPeak.R
mosaics/R/mosaicsFit.R
mosaics/R/mosaicsFitHMM.R
mosaics/R/mosaicsPeak.R
mosaics/R/mosaicsPeakHMM.R
mosaics/R/mosaicsRunAll.R
mosaics/R/readBins.R
mosaics/build
mosaics/build/vignette.rds
mosaics/inst
mosaics/inst/Perl
mosaics/inst/Perl/convert_csem_format.pl
mosaics/inst/Perl/csem_wrapper.pl
mosaics/inst/Perl/extract_coord_PET.pl
mosaics/inst/Perl/extract_coord_SET.pl
mosaics/inst/Perl/process_readfiles_PET.pl
mosaics/inst/Perl/process_readfiles_SET.pl
mosaics/inst/Perl/readfile2wig_PET.pl
mosaics/inst/Perl/readfile2wig_SET.pl
mosaics/inst/doc
mosaics/inst/doc/mosaics-example.R
mosaics/inst/doc/mosaics-example.Rnw
mosaics/inst/doc/mosaics-example.pdf
mosaics/man
mosaics/man/BinData-class.Rd
mosaics/man/MosaicsFit-class.Rd
mosaics/man/MosaicsFitEst-class.Rd
mosaics/man/MosaicsFitParam-class.Rd
mosaics/man/MosaicsHMM-class.Rd
mosaics/man/MosaicsPeak-class.Rd
mosaics/man/MosaicsPeakParam-class.Rd
mosaics/man/TagData-class.Rd
mosaics/man/adjustBoundary.Rd
mosaics/man/constructBins.Rd
mosaics/man/estimates.Rd
mosaics/man/export.Rd
mosaics/man/extractReads.Rd
mosaics/man/findSummit.Rd
mosaics/man/fllterPeak.Rd
mosaics/man/generateWig.Rd
mosaics/man/mosaics-internal.Rd
mosaics/man/mosaics-package.Rd
mosaics/man/mosaicsFit.Rd
mosaics/man/mosaicsFitHMM.Rd
mosaics/man/mosaicsPeak.Rd
mosaics/man/mosaicsPeakHMM.Rd
mosaics/man/mosaicsRunAll.Rd
mosaics/man/readBins.Rd
mosaics/src
mosaics/src/convolution_1S.cpp
mosaics/src/convolution_2S.cpp
mosaics/src/emHMM.cpp
mosaics/src/stack.cpp
mosaics/src/updatePiMat.cpp
mosaics/src/viterbi.cpp
mosaics/vignettes
mosaics/vignettes/Figure4a.pdf
mosaics/vignettes/Figure4b.pdf
mosaics/vignettes/Figure5a.pdf
mosaics/vignettes/Figure5b.pdf
mosaics/vignettes/Figure5c.pdf
mosaics/vignettes/Figure5d.pdf
mosaics/vignettes/GOF_matchLow.pdf
mosaics/vignettes/GOF_rMOM.pdf
mosaics/vignettes/igv.pdf
mosaics/vignettes/mosaics-example.Rnw