Man pages for htSeqTools
Quality Control, Visualization and Processing for High-Throughput Sequencing data
| alignPeaks | Align peaks in a ChIP-Seq experiment by removing the strand... |
| 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... |
| 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... |
| extendRanges | Extend reads or sequences by a user-specified number of... |
| fdrEnrichedCounts | Posterior probability that a certain number of repeats are... |
| filterDuplReads | Detect and filter duplicated reads/sequences. |
| findPeakHeight | FDR and optimal minHeight value estimation for ChIP-Seq peak... |
| giniCoverage | Compute Gini coefficient. |
| gridCover-class | Class "gridCover" |
| htSample | Example ChIP-sequencing data with 2 replicates per group... |
| islandCounts | Find genomic regions with high coverage and count number of... |
| listOverlap | Assess the overlap between two or three lists. |
| mergeRegions | Merge nearby chromosomal regions. |
| plotChrRegions | Plot chromosomal regions of interest |
| plot-methods | Methods for Function plot in Package 'htSeqTools' |
| 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. |
