csaw: ChIP-Seq Analysis with Windows

Share:

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

Author
Aaron Lun <alun@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>
Date of publication
None
Maintainer
Aaron Lun <alun@wehi.edu.au>
License
GPL-3
Version
1.8.0

View on Bioconductor

Man pages

checkBimodality
Check bimodality of regions
clusterFDR
Compute the cluster-level FDR
clusterWindows
Cluster DB windows into clusters
combineTests
Combine statistics across multiple tests
consolidateClusters
Consolidate DB clusters
consolidateSizes
Consolidate window sizes
correlateReads
Compute correlation coefficients between reads
csawUsersGuide
View csaw user's guide
detailRanges
Add annotation to ranges
extractReads
Extract reads from a BAM file
filterWindows
Filtering methods for RangedSummarizedExperiment objects
findMaxima
Find local maxima
getBestTest
Get the best test in a cluster
getPESizes
Compute fragment lengths for paired-end tags
getWidths
Get region widths
maximizeCcf
Find the delay at the maximal CCF
mergeWindows
Merge windows into clusters
normOffsets
Normalize counts between libraries
overlapStats
Compute overlap statistics
paramList
Get or modify readParam lists
profileSites
Profile binding sites
readParam
readParam class and methods
regionCounts
Count reads overlapping each region
scaledAverage
Scaled average abundance
SEmethods
Statistical wrappers for SummarizedExperiment objects
strandedCounts
Get strand-specific counts
upweightSummit
Upweight summits
windowCounts
Count reads overlapping each window
wwhm
Window width at half maximum

Files in this package

csaw/DESCRIPTION
csaw/NAMESPACE
csaw/R
csaw/R/asDGEList.R
csaw/R/basefun.R
csaw/R/checkBimodality.R
csaw/R/clusterFDR.R
csaw/R/clusterWindows.R
csaw/R/combineTests.R
csaw/R/consolidateSizes.R
csaw/R/correlateReads.R
csaw/R/csawUsersGuide.R
csaw/R/detailRanges.R
csaw/R/extractReads.R
csaw/R/filterWindows.R
csaw/R/findMaxima.R
csaw/R/getBestTest.R
csaw/R/getPESizes.R
csaw/R/maximizeCcf.R
csaw/R/mergeWindows.R
csaw/R/normOffsets.R
csaw/R/overlapStats.R
csaw/R/paramList.R
csaw/R/profileSites.R
csaw/R/readParam.R
csaw/R/regionCounts.R
csaw/R/scaledAverage.R
csaw/R/strandedCounts.R
csaw/R/upweightSummit.R
csaw/R/windowCounts.R
csaw/build
csaw/build/vignette.rds
csaw/inst
csaw/inst/CITATION
csaw/inst/NEWS.Rd
csaw/inst/doc
csaw/inst/doc/csaw.Rnw
csaw/inst/doc/csaw.pdf
csaw/inst/doc/csawUserGuide.pdf
csaw/inst/doc/sra2bam.sh
csaw/inst/exdata
csaw/inst/exdata/autogen.R
csaw/inst/exdata/exrange.rds
csaw/inst/exdata/pet.bam
csaw/inst/exdata/pet.bam.bai
csaw/inst/exdata/pet.sam
csaw/inst/exdata/rep1.bam
csaw/inst/exdata/rep1.bam.bai
csaw/inst/exdata/rep2.bam
csaw/inst/exdata/rep2.bam.bai
csaw/inst/tests
csaw/inst/tests/run_all_tests.sh
csaw/inst/tests/simsam.R
csaw/inst/tests/test-best.R
csaw/inst/tests/test-best.Rout.save
csaw/inst/tests/test-bimodal.R
csaw/inst/tests/test-bimodal.Rout.save
csaw/inst/tests/test-ccf.R
csaw/inst/tests/test-ccf.Rout.save
csaw/inst/tests/test-chip.R
csaw/inst/tests/test-chip.Rout.save
csaw/inst/tests/test-cluster.R
csaw/inst/tests/test-cluster.Rout.save
csaw/inst/tests/test-combine.R
csaw/inst/tests/test-combine.Rout.save
csaw/inst/tests/test-cons.R
csaw/inst/tests/test-cons.Rout.save
csaw/inst/tests/test-detail.R
csaw/inst/tests/test-detail.Rout.save
csaw/inst/tests/test-empty.R
csaw/inst/tests/test-empty.Rout.save
csaw/inst/tests/test-filter.R
csaw/inst/tests/test-filter.Rout.save
csaw/inst/tests/test-maxima.R
csaw/inst/tests/test-maxima.Rout.save
csaw/inst/tests/test-merge.R
csaw/inst/tests/test-merge.Rout.save
csaw/inst/tests/test-overlap.R
csaw/inst/tests/test-overlap.Rout.save
csaw/inst/tests/test-pet3.R
csaw/inst/tests/test-pet3.Rout.save
csaw/inst/tests/test-profile.R
csaw/inst/tests/test-profile.Rout.save
csaw/inst/tests/test-region.R
csaw/inst/tests/test-region.Rout.save
csaw/man
csaw/man/SEmethods.Rd
csaw/man/checkBimodality.Rd
csaw/man/clusterFDR.Rd
csaw/man/clusterWindows.Rd
csaw/man/combineTests.Rd
csaw/man/consolidateClusters.Rd
csaw/man/consolidateSizes.Rd
csaw/man/correlateReads.Rd
csaw/man/csawUsersGuide.Rd
csaw/man/detailRanges.Rd
csaw/man/extractReads.Rd
csaw/man/filterWindows.Rd
csaw/man/findMaxima.Rd
csaw/man/getBestTest.Rd
csaw/man/getPESizes.Rd
csaw/man/getWidths.Rd
csaw/man/maximizeCcf.Rd
csaw/man/mergeWindows.Rd
csaw/man/normOffsets.Rd
csaw/man/overlapStats.Rd
csaw/man/paramList.Rd
csaw/man/profileSites.Rd
csaw/man/readParam.Rd
csaw/man/regionCounts.Rd
csaw/man/scaledAverage.Rd
csaw/man/strandedCounts.Rd
csaw/man/upweightSummit.Rd
csaw/man/windowCounts.Rd
csaw/man/wwhm.Rd
csaw/src
csaw/src/Makevars
csaw/src/Makevars.win
csaw/src/annotator.cpp
csaw/src/bam_utils.cpp
csaw/src/bam_utils.h
csaw/src/best_in_cluster.cpp
csaw/src/check_bimodality.cpp
csaw/src/correlate_reads.cpp
csaw/src/csaw.h
csaw/src/find_maxima.cpp
csaw/src/get_cluster_stats.cpp
csaw/src/get_profile.cpp
csaw/src/get_rle_counts.cpp
csaw/src/init.cpp
csaw/src/merge_windows.cpp
csaw/src/pair_reads.cpp
csaw/src/single_reads.cpp
csaw/tests
csaw/tests/test-basic.R
csaw/tests/test-basic.Rout.save
csaw/vignettes
csaw/vignettes/csaw.Rnw