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htSeqTools (version 1.18.0)

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

Description

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.

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Version

Version

1.18.0

License

GPL (>=2)

Maintainer

Oscar Reina

Last Published

February 15th, 2017

Functions in htSeqTools (1.18.0)

mergeRegions

Merge nearby chromosomal regions.
gridCover-class

Class "gridCover"
plot-methods

Methods for Function plot in Package `htSeqTools'
extendRanges

Extend reads or sequences by a user-specified number of bases.
enrichedPeaks

Find peaks in sequencing experiments.
countHitsWindow

Compute number of hits in a moving window along the chromosome.
alignPeaks

Align peaks in a ChIP-Seq experiment by removing the strand specific bias.
ssdCoverage

Standardized SD of the genomic coverage
listOverlap

Assess the overlap between two or three lists.
filterDuplReads

Detect and filter duplicated reads/sequences.
htSample

Example ChIP-sequencing data with 2 replicates per group obtained in two different dates.
stdPeakLocation

Peak density with respect to closest gene.
cmds

Classical Multi-Dimensional Scaling
plotChrRegions

Plot chromosomal regions of interest
cmdsFit

Classical Multi-Dimensional Scaling for a distance matrix
coverageDiff

Compute the difference in coverage between two objects
giniCoverage

Compute Gini coefficient.
enrichedChrRegions

Find chromosomal regions with a high concentration of hits.
findPeakHeight

FDR and optimal minHeight value estimation for ChIP-Seq peak calling with enrichedPeaks.
fdrEnrichedCounts

Posterior probability that a certain number of repeats are higher than expected by chance.
regionsCoverage

Compute coverage on user specified genomic regions.
cmdsFit-class

Class "cmdsFit"
enrichedRegions

Find significantly enriched regions in sequencing experiments.
rowLogRegLRT

Row-wise logistic regression
islandCounts

Find genomic regions with high coverage and count number of reads overlapping each region in each sample