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

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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.

Author
Evarist Planet, Camille Stephan-Otto, Oscar Reina, Oscar Flores, David Rossell
Date of publication
None
Maintainer
Oscar Reina <oscar.reina@irbbarcelona.org>
License
GPL (>=2)
Version
1.22.0

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.

Files in this package

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