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.

AuthorDongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles
Date of publicationNone
MaintainerDongjun Chung <dongjun.chung@gmail.com>
LicenseGPL (>= 2)
Version2.12.0
http://groups.google.com/group/mosaics_user_group

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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