htSeqTools: Quality Control, Visualization and Processing for High-Throughput Sequencing data
Version 1.24.0

We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.

AuthorEvarist Planet, Camille Stephan-Otto, Oscar Reina, Oscar Flores, David Rossell
Bioconductor views QualityControl Sequencing
Date of publicationNone
MaintainerOscar Reina <oscar.reina@irbbarcelona.org>
LicenseGPL (>=2)
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("htSeqTools")

Popular man pages

alignPeaks: Align peaks in a ChIP-Seq experiment by removing the strand...
enrichedChrRegions: Find chromosomal regions with a high concentration of hits.
extendRanges: Extend reads or sequences by a user-specified number of...
findPeakHeight: FDR and optimal minHeight value estimation for ChIP-Seq peak...
giniCoverage: Compute Gini coefficient.
islandCounts: Find genomic regions with high coverage and count number of...
stdPeakLocation: Peak density with respect to closest gene.
See all...

All man pages Function index File listing

Man pages

alignPeaks: Align peaks in a ChIP-Seq experiment by removing the strand...
cmds: Classical Multi-Dimensional Scaling
cmdsFit: Classical Multi-Dimensional Scaling for a distance matrix
cmdsFit-class: Class "cmdsFit"
countHitsWindow: Compute number of hits in a moving window along the...
coverageDiff: Compute the difference in coverage between two objects
enrichedChrRegions: Find chromosomal regions with a high concentration of hits.
enrichedPeaks: Find peaks in sequencing experiments.
enrichedRegions: Find significantly enriched regions in sequencing...
extendRanges: Extend reads or sequences by a user-specified number of...
fdrEnrichedCounts: Posterior probability that a certain number of repeats are...
filterDuplReads: Detect and filter duplicated reads/sequences.
findPeakHeight: FDR and optimal minHeight value estimation for ChIP-Seq peak...
giniCoverage: Compute Gini coefficient.
gridCover-class: Class "gridCover"
htSample: Example ChIP-sequencing data with 2 replicates per group...
islandCounts: Find genomic regions with high coverage and count number of...
listOverlap: Assess the overlap between two or three lists.
mergeRegions: Merge nearby chromosomal regions.
plotChrRegions: Plot chromosomal regions of interest
plot-methods: Methods for Function plot in Package 'htSeqTools'
regionsCoverage: Compute coverage on user specified genomic regions.
rowLogRegLRT: Row-wise logistic regression
ssdCoverage: Standardized SD of the genomic coverage
stdPeakLocation: Peak density with respect to closest gene.

Functions

PeakLocation Man page
PeakLocation,GRanges-method Man page
PeakLocation,RangedData-method Man page
PeakLocation,data.frame-method Man page
PeakLocation-methods Man page
PeakLocationBase Source code
alignPeaks Man page
alignPeaks,GRanges,character-method Man page
alignPeaks,GRangesList,ANY-method Man page
alignPeaks,GRangesList-method Man page
alignPeaks,IRangesList,list-method Man page
alignPeaks,RangedData,character-method Man page
alignPeaks,list,character-method Man page
alignPeaks-methods Man page
basesPerCut2dir Source code
cmds Man page
cmds,GRangesList-method Man page
cmds,list-method Man page
cmds-methods Man page
cmdsFit Man page
cmdsFit,matrix-method Man page
cmdsFit-class Man page
cmdsFit-methods Man page
corRle Source code
corRleList Source code
countDifHitsWindow Source code
countHitsWindow Man page
countHitsWindow,GRanges-method Man page
countHitsWindow,RangedData-method Man page
countHitsWindow-methods Man page
coverageDiff Man page Source code
dist2midpnt Source code
enrichedChrRegions Man page
enrichedChrRegions,GRanges,GRanges-method Man page
enrichedChrRegions,GRanges,missing-method Man page
enrichedChrRegions,RangedData,RangedData-method Man page
enrichedChrRegions,RangedData,missing-method Man page
enrichedChrRegions-methods Man page
enrichedPeaks Man page
enrichedPeaks,GRanges,GRanges,GRanges-method Man page
enrichedPeaks,GRanges,GRanges,missing-method Man page
enrichedPeaks,GRanges,missing,missing-method Man page
enrichedPeaks,RangedData,IRanges,IRanges-method Man page
enrichedPeaks,RangedData,IRanges,missing-method Man page
enrichedPeaks,RangedData,IRangesList,IRangesList-method Man page
enrichedPeaks,RangedData,IRangesList,missing-method Man page
enrichedPeaks,RangedData,RangedData,RangedData-method Man page
enrichedPeaks,RangedData,RangedData,missing-method Man page
enrichedPeaks-methods Man page
enrichedRegions Man page
enrichedRegions,GRanges,GRanges,missing,ANY,ANY-method Man page
enrichedRegions,GRanges,missing,missing,ANY,ANY-method Man page
enrichedRegions,GRangesList,missing,missing,ANY,ANY-method Man page
enrichedRegions,RangedData,RangedData,missing,ANY,ANY-method Man page
enrichedRegions,RangedData,missing,missing,ANY,ANY-method Man page
enrichedRegions,list,missing,missing,ANY,ANY-method Man page
enrichedRegions,missing,missing,GRanges,ANY,ANY-method Man page
enrichedRegions,missing,missing,RangedData,ANY,missing-method Man page
enrichedRegions,missing,missing,RangedData,ANY,numeric-method Man page
enrichedRegions-methods Man page
extendRanges Man page
extendRanges,GRanges-method Man page
extendRanges,GRangesList-method Man page
extendRanges,RangedData-method Man page
extendRanges,list-method Man page
extendRanges-methods Man page
fdrEnrichedCounts Man page Source code
fillRleList Source code
filterDuplReads Man page
filterDuplReads,GRanges-method Man page
filterDuplReads,GRangesList-method Man page
filterDuplReads,RangedData-method Man page
filterDuplReads,list-method Man page
filterDuplReads-methods Man page
findPeakHeight Man page
findPeakHeight,GRanges,GRanges,GRanges-method Man page
findPeakHeight,RangedData,IRangesList,IRangesList-method Man page
findPeakHeight,RangedData,RangedData,RangedData-method Man page
findPeakHeight,RangedData,Rle,Rle-method Man page
findPeakHeight-methods Man page
getCover Man page
getCover,gridCover-method Man page
getGrid Source code
getGridList Source code
getViewsInfo Man page
getViewsInfo,gridCover-method Man page
giniCoverage Man page
giniCoverage,GRanges,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,GRanges,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,GRanges,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,GRanges,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage,list,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,list,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,list,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,list,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage-methods Man page
gridCover-class Man page
gridCoverage Man page Source code
hitsPerCut Source code
hitsPerCut2dir Source code
htSample Man page
ilogit Source code
islandCounts Man page
islandCounts,GRanges-method Man page
islandCounts,GRangesList-method Man page
islandCounts,RangedData-method Man page
islandCounts,list-method Man page
islandCounts-methods Man page
lines,gridCover-method Man page
listOverlap Man page
listOverlap,character,character,character,character-method Man page
listOverlap,character,character,missing,character-method Man page
listOverlap,factor,character,missing,missing-method Man page
listOverlap-methods Man page
logit Source code
meanRandomHits Source code
mergeRegions Man page
mergeRegions,GRanges-method Man page
mergeRegions,IRanges-method Man page
mergeRegions,RangedData-method Man page
mergeRegions,RleViews-method Man page
mergeRegions,data.frame-method Man page
mergeRegions,matrix-method Man page
mergeRegions-methods Man page
mergeRegionsCore Source code
plot,cmdsFit,ANY-method Man page
plot,cmdsFit-method Man page
plot,gridCover,ANY-method Man page
plot,gridCover-method Man page
plotChrRegions Man page Source code
plotMeanCoverage Man page
plotMeanCoverage,RleList,RangedData-method Man page
plotMeanCoverage-methods Man page
plotminHeight Man page Source code
randomHits2groups Source code
randomHitsWindow Source code
regionsCoverage Man page
regionsCoverage,ANY,ANY,ANY,RleList-method Man page
regionsCoverage-methods Man page
rowLogRegLRT Man page Source code
show,gridCover-method Man page
ssdCoverage Man page
ssdCoverage,GRanges-method Man page
ssdCoverage,GRangesList-method Man page
ssdCoverage,IRangesList-method Man page
ssdCoverage,RangedData-method Man page
ssdCoverage,list-method Man page
ssdCoverage-methods Man page
stdGrid Man page
stdGrid,gridCover-method Man page
stdGrid-methods Man page
stdPeakLocation Man page
stdPeakLocation,GRanges-method Man page
stdPeakLocation,RangedData-method Man page
stdPeakLocation,data.frame-method Man page
stdPeakLocation-methods Man page
stdPeakLocationBase Source code
tabDuplReads Man page
tabDuplReads,GRanges-method Man page
tabDuplReads,GRangesList-method Man page
tabDuplReads,RangedData-method Man page
tabDuplReads,list-method Man page
tabDuplReads-methods Man page

Files

ChangeLog
DESCRIPTION
NAMESPACE
R
R/ClassDefinitions.R
R/GenericDefs.R
R/alignPeaks.R
R/cmds.R
R/cmdsFit-class.R
R/countRepeats.R
R/coverageDiff.R
R/enrichedChrRegions.R
R/enrichedPeaks.R
R/enrichedRegions.R
R/extendRanges.R
R/fdrEnrichedCounts.R
R/filterDuplReads.R
R/findPeakHeight.R
R/giniCoverage.R
R/gridCover-methods.R
R/islandCounts.R
R/listOverlap.R
R/mergeRegions.R
R/plotChrRegions.R
R/plotMeanCoverage.R
R/regionsCoverage.R
R/rowLogRegLRT.R
R/ssdCoverage.R
R/stdPeakLocation.R
R/tabDuplReads.R
build
build/vignette.rds
data
data/datalist
data/htSample.RData
inst
inst/NEWS
inst/doc
inst/doc/htSeqTools.R
inst/doc/htSeqTools.Rnw
inst/doc/htSeqTools.pdf
man
man/alignPeaks.Rd
man/cmds.Rd
man/cmdsFit-class.Rd
man/cmdsFit.Rd
man/countHitsWindow.Rd
man/coverageDiff.Rd
man/enrichedChrRegions.Rd
man/enrichedPeaks.Rd
man/enrichedRegions.Rd
man/extendRanges.Rd
man/fdrEnrichedCounts.Rd
man/filterDuplReads.Rd
man/findPeakHeight.Rd
man/giniCoverage.Rd
man/gridCover-class.Rd
man/htSample.Rd
man/islandCounts.Rd
man/listOverlap.Rd
man/mergeRegions.Rd
man/plot-methods.Rd
man/plotChrRegions.Rd
man/regionsCoverage.Rd
man/rowLogRegLRT.Rd
man/ssdCoverage.Rd
man/stdPeakLocation.Rd
vignettes
vignettes/htSeqTools.Rnw
vignettes/references.bib
htSeqTools documentation built on May 20, 2017, 9:26 p.m.

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