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.

Author
Apratim Mitra, Jiuzhou Song
Date of publication
2013-11-25 21:48:57
Maintainer
Apratim Mitra <amitra83@umd.edu>, Jiuzhou Song <songj88@umd.edu>
License
GPL (>= 2)
Version
1.0.3

View on R-Forge

Man pages

checkFolderHierarchy
Check folder organization
compareWithControl
Compare ChIP to Control
controlFDR
FDR Estimation with Control
gabp_peaks
Peak Calling results on GABP data
gapDiagnostic
Function to Select Suitable Gap Size
gapPeaks
Concatenate Peaks within a User-specified Distance
getConfidenceInterval
Get confidence intervals of Wavelet coefficients after Monte...
getPeakReads
Get Reads Within a List of Specified Locations
getPeakReads_batch
Get Reads Within a List of Specified Locations in Batch
getThresholdDistribution
Wavelet Threshold Estimation
noControlFDR
FDR Estimation without Control
preprocess
Data preprocessing
randomizedBackground
Randomized Background Estimation
waveletThresholding
Perform Wavelet CWT Thresholding
waveseq
Run WaveSeq Analysis Pipeline
WaveSeqR-package
WaveSeq: A Wavelet-based Algorithm for Detecting Histone...

Files in this package

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