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

alignPeaksAlign peaks in a ChIP-Seq experiment by removing the strand...
cmdsClassical Multi-Dimensional Scaling
cmdsFitClassical Multi-Dimensional Scaling for a distance matrix
cmdsFit-classClass "cmdsFit"
countHitsWindowCompute number of hits in a moving window along the...
coverageDiffCompute the difference in coverage between two objects
enrichedChrRegionsFind chromosomal regions with a high concentration of hits.
enrichedPeaksFind peaks in sequencing experiments.
enrichedRegionsFind significantly enriched regions in sequencing...
extendRangesExtend reads or sequences by a user-specified number of...
fdrEnrichedCountsPosterior probability that a certain number of repeats are...
filterDuplReadsDetect and filter duplicated reads/sequences.
findPeakHeightFDR and optimal minHeight value estimation for ChIP-Seq peak...
giniCoverageCompute Gini coefficient.
gridCover-classClass "gridCover"
htSampleExample ChIP-sequencing data with 2 replicates per group...
islandCountsFind genomic regions with high coverage and count number of...
listOverlapAssess the overlap between two or three lists.
mergeRegionsMerge nearby chromosomal regions.
plotChrRegionsPlot chromosomal regions of interest
plot-methodsMethods for Function plot in Package 'htSeqTools'
regionsCoverageCompute coverage on user specified genomic regions.
rowLogRegLRTRow-wise logistic regression
ssdCoverageStandardized SD of the genomic coverage
stdPeakLocationPeak density with respect to closest gene.
htSeqTools documentation built on May 6, 2019, 3:39 a.m.