Package: csaw 1.41.2

Aaron Lun

csaw: ChIP-Seq Analysis with Windows

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

Authors:Aaron Lun [aut, cre], Gordon Smyth [aut]

csaw_1.41.2.tar.gz
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csaw.pdf |csaw.html✨
csaw/json (API)
NEWS

# Install 'csaw' in R:

install.packages('csaw', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:csaw-1.41.1(bioc 3.21)csaw-1.40.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

multiplecomparison chipseq normalization sequencing coverage genetics annotation differentialpeakcalling curl bzip2 xz-utils zlib cpp

8.32 score 7 packages 498 scripts 893 downloads 29 mentions 54 exports 47 dependencies

Last updated 3 days agofrom:75cff36a84. Checks:1 OK, 4 NOTE, 6 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 30 2025
R-4.5-win-x86_64	NOTE	Jan 30 2025
R-4.5-mac-x86_64	WARNING	Jan 30 2025
R-4.5-mac-aarch64	WARNING	Jan 30 2025
R-4.5-linux-x86_64	NOTE	Jan 30 2025
R-4.4-win-x86_64	NOTE	Jan 30 2025
R-4.4-mac-x86_64	WARNING	Jan 30 2025
R-4.4-mac-aarch64	WARNING	Jan 30 2025
R-4.3-win-x86_64	NOTE	Jan 30 2025
R-4.3-mac-x86_64	WARNING	Jan 30 2025
R-4.3-mac-aarch64	WARNING	Jan 30 2025

Exports:asDGEList calculateCPM checkBimodality clusterFDR clusterWindows clusterWindowsList combineOverlaps combineTests consolidateOverlaps consolidateTests consolidateWindows controlClusterFDR correlateReads csawUsersGuide detailRanges empiricalFDR empiricalOverlaps extractReads filterWindows filterWindowsControl filterWindowsGlobal filterWindowsLocal filterWindowsProportion findMaxima findOverlapsList getBestOverlaps getBestTest getPESizes getWidths maximizeCcf mergeResults mergeResultsList mergeWindows mergeWindowsList minimalTests mixedClusters mixedOverlaps mixedTests normFactors normOffsets overlapResults overlapResultsList profileSites readParam reform regionCounts scaleControlFilter scaledAverage show strandedCounts summitOverlaps upweightSummit windowCounts wwhm

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray edgeR formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r lattice limma locfit Matrix MatrixGenerics matrixStats metapod mime openssl R6 Rcpp Rhtslib Rsamtools S4Arrays S4Vectors snow SparseArray statmod SummarizedExperiment sys UCSC.utils XVector

Introducing the csaw package

Aaron Lun

Rendered fromcsaw.Rmdusingknitr::rmarkdownon Jan 30 2025.

Last update: 2020-11-26
Started: 2019-02-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate CPM	calculateCPM
Check bimodality of regions	checkBimodality
Reporting cluster-level direction in 'csaw'	cluster-direction
Compute the cluster-level FDR	clusterFDR controlClusterFDR
Cluster DB windows into clusters	clusterWindows
Consolidate DB clusters	clusterWindowsList
Combine statistics across multiple tests	combineTests
Compute correlation coefficients between reads	correlateReads
View csaw user's guide	csaw csawUsersGuide
Defunct functions	consolidateOverlaps consolidateTests consolidateWindows defunct filterWindows
Add annotation to ranges	detailRanges
Control the empirical FDR	empiricalFDR
Extract reads from a BAM file	extractReads
Filtering methods for RangedSummarizedExperiment objects	filterWindowsControl filterWindowsGlobal filterWindowsLocal filterWindowsProportion scaleControlFilter
Find local maxima	findMaxima
Get the best test in a cluster	getBestTest
Compute fragment lengths for paired-end tags	getPESizes
Get region widths	getWidths
Find the delay at the maximal CCF	maximizeCcf
Merge windows into clusters	mergeWindows
Consolidate window sizes	findOverlapsList mergeWindowsList
Require rejection of a minimal number of tests	minimalTests
Tests for mixed DB clusters	mixedClusters mixedTests
Scaling normalization across libraries	normFactors
Normalize trended biases across libraries	normOffsets
Combine statistics for overlap-based clusters	combineOverlaps empiricalOverlaps getBestOverlaps mixedOverlaps overlapStats summitOverlaps
Profile binding sites	profileSites
readParam class and methods	$,readParam-method readParam readParam-class reform reform,readParam-method show,readParam-method
Count reads overlapping each region	regionCounts
Wrappers to get region-level results	mergeResults overlapResults
Wrappers to combine multiple analyses	mergeResultsList overlapResultsList
Scaled average abundance	scaledAverage
SummarizedExperiment to DGEList	asDGEList asDGEList,SummarizedExperiment-method
Get strand-specific counts	strandedCounts
Upweight summits	upweightSummit
Count reads overlapping each window	windowCounts
Window width at half maximum	wwhm