WaveSeqR: A Wavelet-based Method for ChIP-Seq peak calling
Version 1.0.3

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
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("WaveSeqR", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

checkFolderHierarchy: Check folder organization
gapDiagnostic: Function to Select Suitable Gap Size
gapPeaks: Concatenate Peaks within a User-specified Distance
noControlFDR: FDR Estimation without Control
randomizedBackground: Randomized Background Estimation
waveseq: Run WaveSeq Analysis Pipeline
WaveSeqR-package: WaveSeq: A Wavelet-based Algorithm for Detecting Histone...
See all...

All man pages Function index File listing

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...

Functions

Files

DESCRIPTION
NAMESPACE
R
R/checkFolderHierarchy.R
R/compareWithControl.R
R/controlFDR.R
R/gapDiagnostic.R
R/gapPeaks.R
R/getConfidenceInterval.R
R/getPeakReads.R
R/getPeakReads_batch.R
R/getThresholdDistribution.R
R/noControlFDR.R
R/preprocess.R
R/randomizedBackground.R
R/setenvar.R
R/waveletThresholding.R
R/waveseq.R
build
build/vignette.rds
data
data/gabp_peaks.rda
exec
exec/bed2graph.pl
exec/get_chr_info.pl
exec/pad_graph.pl
exec/rem_dup_reads.pl
inst
inst/CITATION
inst/doc
inst/doc/waveSeqR.Rnw
inst/doc/waveSeqR.pdf
inst/extdata
inst/extdata/gabp_valouev2008_chr22-15m-30m-pad.graph
inst/extdata/padgraph
inst/extdata/padgraph/chrlist_GABP_valouev_chr22_control.txt
inst/extdata/padgraph/chrlist_GABP_valouev_chr22_nocontrol.txt
inst/extdata/rxnoip_valouev2008_chr22-15m-30m-pad.graph
inst/extdata/thresdist
inst/extdata/thresdist/thres_avg_morlet_GABP_valouev_chr22_control.txt
inst/extdata/thresdist/thres_avg_morlet_GABP_valouev_chr22_nocontrol.txt
inst/extdata/thresdist/thres_std_morlet_GABP_valouev_chr22_control.txt
inst/extdata/thresdist/thres_std_morlet_GABP_valouev_chr22_nocontrol.txt
man
man/WaveSeqR-package.Rd
man/checkFolderHierarchy.Rd
man/compareWithControl.Rd
man/controlFDR.Rd
man/gabp_peaks.Rd
man/gapDiagnostic.Rd
man/gapPeaks.Rd
man/getConfidenceInterval.Rd
man/getPeakReads.Rd
man/getPeakReads_batch.Rd
man/getThresholdDistribution.Rd
man/noControlFDR.Rd
man/preprocess.Rd
man/randomizedBackground.Rd
man/waveletThresholding.Rd
man/waveseq.Rd
vignettes
vignettes/waveSeqR.Rnw
WaveSeqR documentation built on May 21, 2017, 1:11 a.m.

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