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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
1.6.1
1.4.0
1.2.1
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Version
1.6.1
License
GPL-3
Maintainer
Aaron Lun
Last Published
March 12th, 2016
Functions in csaw (1.6.1)
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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