Package: chipseq 1.57.0

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]

chipseq_1.57.0.tar.gz
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chipseq.pdf |chipseq.html✨
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-1.57.0(bioc 3.21)chipseq-1.56.0(bioc 3.20)

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

6.39 score 5 packages 91 scripts 958 downloads 9 mentions 12 exports 55 dependencies

Last updated 2 months agofrom:205b179048. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	WARNING	Nov 29 2024
R-4.5-linux-x86_64	WARNING	Nov 29 2024
R-4.4-win-x86_64	WARNING	Nov 29 2024
R-4.4-mac-x86_64	WARNING	Nov 29 2024
R-4.4-mac-aarch64	WARNING	Nov 29 2024
R-4.3-win-x86_64	WARNING	Nov 29 2024
R-4.3-mac-x86_64	WARNING	Nov 29 2024
R-4.3-mac-aarch64	WARNING	Nov 29 2024

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

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray deldir formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr hwriter interp IRanges jpeg jsonlite lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats mime openssl png pwalign R6 RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors ShortRead snow SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

Some Basic Analysis of ChIP-Seq Data

Oluwabukola Bamigbade

Rendered fromWorkflow.Rmdusingknitr::rmarkdownon Nov 29 2024.

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