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csaw (version 1.6.1)

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

1.6.1

License

GPL-3

Maintainer

Aaron Lun

Last Published

February 15th, 2017

Functions in csaw (1.6.1)

maximizeCcf

Find the delay at the maximal CCF
normOffsets

Normalize counts between libraries
combineTests

Combine statistics across multiple tests
overlapStats

Compute overlap statistics
extractReads

Extract reads from a BAM file
upweightSummit

Upweight summits
clusterFDR

Compute the cluster-level FDR
getWidths

Get region widths
consolidateClusters

Consolidate DB clusters
getPESizes

Compute fragment lengths for paired-end tags
scaledAverage

Scaled average abundance
detailRanges

Add annotation to ranges
profileSites

Profile binding sites
getBestTest

Get the best test in a cluster
regionCounts

Count reads overlapping each region
consolidateSizes

Consolidate window sizes
checkBimodality

Check bimodality of regions
readParam

readParam class and methods
wwhm

Window width at half maximum
mergeWindows

Merge windows into clusters
windowCounts

Count reads overlapping each window
findMaxima

Find local maxima
filterWindows

Filtering methods for RangedSummarizedExperiment objects
strandedCounts

Get strand-specific counts
csawUsersGuide

View csaw user's guide
correlateReads

Compute correlation coefficients between reads
Parameter list methods

Get or modify readParam lists
SEmethods

Statistical wrappers for SummarizedExperiment objects
clusterWindows

Cluster DB windows into clusters