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

## Documentation for package ‘htSeqTools’ version 1.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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