We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.
|Author||Evarist Planet, Camille Stephan-Otto, Oscar Reina, Oscar Flores, David Rossell|
|Date of publication||None|
|Maintainer||Oscar Reina <firstname.lastname@example.org>|
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.