Package: GreyListChIP 1.39.0

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_1.39.0.tar.gz
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GreyListChIP.pdf |GreyListChIP.html✨
GreyListChIP/json (API)
NEWS

# 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-1.39.0(bioc 3.21)GreyListChIP-1.38.0(bioc 3.20)

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

chipseq alignment preprocessing differentialpeakcalling sequencing genomeannotation coverage

4.93 score 4 packages 10 scripts 1.8k downloads 2 mentions 9 exports 51 dependencies

Last updated 4 months agofrom:daa5333f90. Checks:5 OK, 3 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 17 2025
R-4.5-win	NOTE	Feb 17 2025
R-4.5-mac	NOTE	Feb 17 2025
R-4.5-linux	NOTE	Feb 17 2025
R-4.4-win	OK	Feb 17 2025
R-4.4-mac	OK	Feb 17 2025
R-4.3-win	OK	Feb 17 2025
R-4.3-mac	OK	Feb 17 2025

Exports:calcThreshold countReads export getKaryotype greyListBS loadKaryotype makeGreyList setRegions show

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

Generating Grey Lists from Input Libraries

Rendered fromGreyList-demo.Rnwusingutils::Sweaveon Feb 17 2025.

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