Package: chipseq 1.63.0

Bioconductor Package Maintainer

chipseq: chipseq: A package for analyzing chipseq data

Tools for helping process short read data for chipseq experiments.

Authors:Deepayan Sarkar [aut], Robert Gentleman [aut], Michael Lawrence [aut], Zizhen Yao [aut], Oluwabukola Bamigbade [ctb], Bioconductor Package Maintainer [cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
chipseq/json (API)

# Install 'chipseq' in R:

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

Datasets:

cstest - A test ChIP-Seq dataset

On BioConductor:chipseq-1.63.0(bioc 3.24)chipseq-1.62.0(bioc 3.23)

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

chipseq sequencing coverage qualitycontrol dataimport

6.08 score 2 packages 95 scripts 1.2k downloads 9 mentions 12 exports 45 dependencies

Last updated from:450a128cfa. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	272
linux-devel-arm64	WARNING	340
linux-devel-x86_64	WARNING	520
source / vignettes	OK	442
linux-release-arm64	WARNING	356
linux-release-x86_64	WARNING	431
macos-release-arm64	WARNING	233
macos-release-x86_64	WARNING	516
macos-oldrel-arm64	WARNING	254
macos-oldrel-x86_64	WARNING	456
windows-devel	WARNING	300
windows-release	WARNING	309
windows-oldrel	WARNING	321
wasm-release	OK	253

Exports:basesCovered chipseqFilter coverageplot densityCorr diffPeakSummary estimate.mean.fraglen islandDepthPlot laneSubsample peakCutoff peakSummary sparse.density subsetSummary

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo codetools cpp11 crayon DelayedArray deldir formatR futile.logger futile.options generics GenomicAlignments GenomicRanges hwriter interp IRanges jpeg lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats png pwalign RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors Seqinfo ShortRead snow SparseArray SummarizedExperiment XVector

Some Basic Analysis of ChIP-Seq Data

Rendered fromWorkflow.Rmdusingknitr::rmarkdown

Last update: 2023-04-13
Started: 2023-04-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filtering ChIP-seq reads	chipseqFilter
Plot coverage on a small interval.	coverageplot
A test ChIP-Seq dataset	cstest
A function to identify and produce summary statistics for differentially expressed peaks.	diffPeakSummary diffPeakSummary,RleViewsList,RleViewsList-method
Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.	basesCovered densityCorr densityCorr,GenomicRanges densityCorr,list estimate.mean.fraglen estimate.mean.fraglen,AlignedRead-method estimate.mean.fraglen,GRanges-method sparse.density
Plot island depth distribution	islandDepthPlot
Subsample short read alignment locations	laneSubsample
Calculate a peak cutoff	peakCutoff
Summarizing peak sets	peakSummary peakSummary,RleViews-method peakSummary,RleViewsList-method peakSummary-methods
Compute summaries for cumulative subsets of a short-read data set.	subsetSummary