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. |
[,gridCover,ANY,ANY | Class "gridCover" |
[-method | Class "gridCover" |