Package: GreyListChIP 1.45.0

Matt Eldridge

GreyListChIP: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.

Authors:Matt Eldridge [cre], Gord Brown [aut]

GreyListChIP_1.45.0.tar.gz
GreyListChIP_1.45.0.zip(r-4.7)GreyListChIP_1.45.0.zip(r-4.6)GreyListChIP_1.45.0.zip(r-4.5)
GreyListChIP_1.45.0.tgz(r-4.6-any)GreyListChIP_1.45.0.tgz(r-4.5-any)
GreyListChIP_1.45.0.tar.gz(r-4.7-any)GreyListChIP_1.45.0.tar.gz(r-4.6-any)
GreyListChIP_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GreyListChIP/json (API)

# Install 'GreyListChIP' in R:

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

Datasets:

ce10.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
ce11.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
dm3.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
dm6.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
grch37.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
grch38.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
greyList - A sample 'GreyList' object for use in examples.
hg19.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
hg38.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
mm10.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
mm9.blacklist - A 'GRanges' object representing ENCODE signal artefact or "black list" regions.

On BioConductor:GreyListChIP-1.45.0(bioc 3.24)GreyListChIP-1.44.0(bioc 3.23)

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

chipseq alignment preprocessing differentialpeakcalling sequencing genomeannotation coverage

5.09 score 4 packages 17 scripts 2 mentions 9 exports 51 dependencies

Last updated from:47016f1950. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	235
linux-devel-x86_64	NOTE	450
source / vignettes	OK	318
linux-release-x86_64	NOTE	406
macos-release-arm64	NOTE	241
macos-oldrel-arm64	NOTE	280
windows-devel	NOTE	354
windows-release	NOTE	347
windows-oldrel	NOTE	334
wasm-release	OK	193

Exports:calcThreshold countReads export getKaryotype greyListBS loadKaryotype makeGreyList setRegions show

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cigarillo codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice MASS Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys XML XVector yaml

Generating Grey Lists from Input Libraries

Rendered fromGreyList-demo.Rnwusingutils::Sweave

Last update: 2020-07-29
Started: 2015-01-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Read Count Threshold	calcThreshold calcThreshold,GreyList-method
A 'GRanges' object representing ENCODE signal artefact or "black list" regions.	ce10.blacklist ce11.blacklist dm3.blacklist dm6.blacklist grch37.blacklist grch38.blacklist hg19.blacklist hg38.blacklist mm10.blacklist mm9.blacklist
Count reads from a 'BamFile'	countReads countReads,GreyList-method
Replace the karyotype of a 'GreyList' object	getKaryotype getKaryotype,GreyList-method
A sample 'GreyList' object for use in examples.	greyList
'"GreyList"' Objects	export,GreyList,character,missing-method GreyList GreyList-class initialize,GreyList,BSgenome-method show,GreyList-method
Construct a grey list with default arguments	greyListBS
Load a karyotype from a file	loadKaryotype loadKaryotype,GreyList-method
Generate a grey list from a 'GreyList' object	makeGreyList makeGreyList,GreyList-method
Replace the set of regions of a 'GreyList' object	setRegions setRegions,GreyList-method