alignPeaks              Align peaks in a ChIP-Seq experiment by
                        removing the strand specific bias.
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 chromosome.
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 experiments.
extendRanges            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.
findPeakHeight          FDR and optimal minHeight value estimation for
                        ChIP-Seq peak calling with enrichedPeaks.
giniCoverage            Compute Gini coefficient.
gridCover-class         Class "gridCover"
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
listOverlap             Assess the overlap between two or three lists.
mergeRegions            Merge nearby chromosomal regions.
plot,cmdsFit-method     Methods for Function plot in Package
                        'htSeqTools'
plotChrRegions          Plot chromosomal regions of interest
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.
