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csaw (version 1.2.1)

ChIP-seq analysis with windows

Description

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

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Version

Version

1.2.1

License

GPL-3

Maintainer

Aaron Lun

Last Published

February 15th, 2017

Functions in csaw (1.2.1)

correlateReads

Compute correlation coefficients between reads
csawUsersGuide

View csaw user's guide
normalizeCounts

Normalize counts between libraries
overlapStats

Compute overlap statistics
extractReads

Extract reads from a BAM file
filterWindows

Filtering methods for SummarizedExperiment objects
readParam

readParam class and methods
regionCounts

Count reads overlapping each region
dumpPE

Dump paired-end data to file
makeExtVector

Make an extVector object
detailRanges

Add annotation to ranges
scaledAverage

Scaled average abundance
mergeWindows

Merge windows into clusters
SEmethods

Statistical wrappers for SummarizedExperiment objects
findMaxima

Find local maxima
getBestTest

Get the best test in a cluster
Parameter list methods

Get or modify readParam lists
profileSites

Profile binding sites
strandedCounts

Get strand-specific counts
upweightSummit

Upweight summits
consolidateSizes

Consolidate window sizes
getPESizes

Compute fragment lengths for paired-end tags
combineTests

Combine statistics across multiple tests
getWidths

Get region widths
wwhm

Window width at half maximum
windowCounts

Count reads overlapping each window