WaveSeqR: A Wavelet-based Method for ChIP-Seq peak calling

Sensitive peak-caller for detecting punctate and diffuse enrichment regions that utilizes the continuous wavelet transform framework.

AuthorApratim Mitra, Jiuzhou Song
Date of publication2013-11-25 21:48:57
MaintainerApratim Mitra <amitra83@umd.edu>, Jiuzhou Song <songj88@umd.edu>
LicenseGPL (>= 2)
Version1.0.3

View on R-Forge

Files

WaveSeqR/DESCRIPTION
WaveSeqR/NAMESPACE
WaveSeqR/R
WaveSeqR/R/checkFolderHierarchy.R WaveSeqR/R/compareWithControl.R WaveSeqR/R/controlFDR.R WaveSeqR/R/gapDiagnostic.R WaveSeqR/R/gapPeaks.R WaveSeqR/R/getConfidenceInterval.R WaveSeqR/R/getPeakReads.R WaveSeqR/R/getPeakReads_batch.R WaveSeqR/R/getThresholdDistribution.R WaveSeqR/R/noControlFDR.R WaveSeqR/R/preprocess.R WaveSeqR/R/randomizedBackground.R WaveSeqR/R/setenvar.R WaveSeqR/R/waveletThresholding.R WaveSeqR/R/waveseq.R
WaveSeqR/build
WaveSeqR/build/vignette.rds
WaveSeqR/data
WaveSeqR/data/gabp_peaks.rda
WaveSeqR/exec
WaveSeqR/exec/bed2graph.pl
WaveSeqR/exec/get_chr_info.pl
WaveSeqR/exec/pad_graph.pl
WaveSeqR/exec/rem_dup_reads.pl
WaveSeqR/inst
WaveSeqR/inst/CITATION
WaveSeqR/inst/doc
WaveSeqR/inst/doc/waveSeqR.Rnw
WaveSeqR/inst/doc/waveSeqR.pdf
WaveSeqR/inst/extdata
WaveSeqR/inst/extdata/gabp_valouev2008_chr22-15m-30m-pad.graph
WaveSeqR/inst/extdata/padgraph
WaveSeqR/inst/extdata/padgraph/chrlist_GABP_valouev_chr22_control.txt
WaveSeqR/inst/extdata/padgraph/chrlist_GABP_valouev_chr22_nocontrol.txt
WaveSeqR/inst/extdata/rxnoip_valouev2008_chr22-15m-30m-pad.graph
WaveSeqR/inst/extdata/thresdist
WaveSeqR/inst/extdata/thresdist/thres_avg_morlet_GABP_valouev_chr22_control.txt
WaveSeqR/inst/extdata/thresdist/thres_avg_morlet_GABP_valouev_chr22_nocontrol.txt
WaveSeqR/inst/extdata/thresdist/thres_std_morlet_GABP_valouev_chr22_control.txt
WaveSeqR/inst/extdata/thresdist/thres_std_morlet_GABP_valouev_chr22_nocontrol.txt
WaveSeqR/man
WaveSeqR/man/WaveSeqR-package.Rd WaveSeqR/man/checkFolderHierarchy.Rd WaveSeqR/man/compareWithControl.Rd WaveSeqR/man/controlFDR.Rd WaveSeqR/man/gabp_peaks.Rd WaveSeqR/man/gapDiagnostic.Rd WaveSeqR/man/gapPeaks.Rd WaveSeqR/man/getConfidenceInterval.Rd WaveSeqR/man/getPeakReads.Rd WaveSeqR/man/getPeakReads_batch.Rd WaveSeqR/man/getThresholdDistribution.Rd WaveSeqR/man/noControlFDR.Rd WaveSeqR/man/preprocess.Rd WaveSeqR/man/randomizedBackground.Rd WaveSeqR/man/waveletThresholding.Rd WaveSeqR/man/waveseq.Rd
WaveSeqR/vignettes
WaveSeqR/vignettes/waveSeqR.Rnw

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

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