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


[Up] [Top]

Documentation for package ‘htSeqTools’ version 1.22.0

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.