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

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
Date of publicationNone
MaintainerOscar Reina <oscar.reina@irbbarcelona.org>
LicenseGPL (>=2)
Version1.22.0

View on Bioconductor

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

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,list,character-method Man page
alignPeaks-methods Man page
alignPeaks,RangedData,character-method Man page
cmds Man page
cmdsFit Man page
cmdsFit-class Man page
cmdsFit,matrix-method Man page
cmdsFit-methods Man page
cmds,GRangesList-method Man page
cmds,list-method Man page
cmds-methods Man page
countHitsWindow Man page
countHitsWindow,GRanges-method Man page
countHitsWindow-methods Man page
countHitsWindow,RangedData-method Man page
coverageDiff Man page
enrichedChrRegions Man page
enrichedChrRegions,GRanges,GRanges-method Man page
enrichedChrRegions,GRanges,missing-method Man page
enrichedChrRegions-methods Man page
enrichedChrRegions,RangedData,missing-method Man page
enrichedChrRegions,RangedData,RangedData-method 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-methods Man page
enrichedPeaks,RangedData,IRanges,IRanges-method Man page
enrichedPeaks,RangedData,IRangesList,IRangesList-method Man page
enrichedPeaks,RangedData,IRangesList,missing-method Man page
enrichedPeaks,RangedData,IRanges,missing-method Man page
enrichedPeaks,RangedData,RangedData,missing-method Man page
enrichedPeaks,RangedData,RangedData,RangedData-method Man page
enrichedRegions Man page
enrichedRegions,GRanges,GRanges,missing,ANY,ANY-method Man page
enrichedRegions,GRangesList,missing,missing,ANY,ANY-method Man page
enrichedRegions,GRanges,missing,missing,ANY,ANY-method Man page
enrichedRegions,list,missing,missing,ANY,ANY-method Man page
enrichedRegions-methods 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,RangedData,missing,missing,ANY,ANY-method Man page
enrichedRegions,RangedData,RangedData,missing,ANY,ANY-method Man page
extendRanges Man page
extendRanges,GRangesList-method Man page
extendRanges,GRanges-method Man page
extendRanges,list-method Man page
extendRanges-methods Man page
extendRanges,RangedData-method Man page
fdrEnrichedCounts Man page
filterDuplReads Man page
filterDuplReads,GRangesList-method Man page
filterDuplReads,GRanges-method Man page
filterDuplReads,list-method Man page
filterDuplReads-methods Man page
filterDuplReads,RangedData-method Man page
findPeakHeight Man page
findPeakHeight,GRanges,GRanges,GRanges-method Man page
findPeakHeight-methods Man page
findPeakHeight,RangedData,IRangesList,IRangesList-method Man page
findPeakHeight,RangedData,RangedData,RangedData-method Man page
findPeakHeight,RangedData,Rle,Rle-method Man page
getCover Man page
getCover,gridCover-method Man page
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,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
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
gridCoverage Man page
gridCover-class Man page
htSample Man page
islandCounts Man page
islandCounts,GRangesList-method Man page
islandCounts,GRanges-method Man page
islandCounts,list-method Man page
islandCounts-methods Man page
islandCounts,RangedData-method 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
mergeRegions Man page
mergeRegions,data.frame-method Man page
mergeRegions,GRanges-method Man page
mergeRegions,IRanges-method Man page
mergeRegions,matrix-method Man page
mergeRegions-methods Man page
mergeRegions,RangedData-method Man page
mergeRegions,RleViews-method Man page
PeakLocation Man page
PeakLocation,data.frame-method Man page
PeakLocation,GRanges-method Man page
PeakLocation-methods Man page
PeakLocation,RangedData-method Man page
plotChrRegions Man page
plot,cmdsFit,ANY-method Man page
plot,cmdsFit-method Man page
plot,gridCover,ANY-method Man page
plot,gridCover-method Man page
plotMeanCoverage Man page
plotMeanCoverage-methods Man page
plotMeanCoverage,RleList,RangedData-method Man page
plotminHeight Man page
regionsCoverage Man page
regionsCoverage,ANY,ANY,ANY,RleList-method Man page
regionsCoverage-methods Man page
rowLogRegLRT Man page
show,gridCover-method Man page
ssdCoverage Man page
ssdCoverage,GRangesList-method Man page
ssdCoverage,GRanges-method Man page
ssdCoverage,IRangesList-method Man page
ssdCoverage,list-method Man page
ssdCoverage-methods Man page
ssdCoverage,RangedData-method Man page
stdGrid Man page
stdGrid,gridCover-method Man page
stdGrid-methods Man page
stdPeakLocation Man page
stdPeakLocation,data.frame-method Man page
stdPeakLocation,GRanges-method Man page
stdPeakLocation-methods Man page
stdPeakLocation,RangedData-method Man page
tabDuplReads Man page
tabDuplReads,GRangesList-method Man page
tabDuplReads,GRanges-method Man page
tabDuplReads,list-method Man page
tabDuplReads-methods Man page
tabDuplReads,RangedData-method Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.