Package: chipenrich 2.31.0

Kai Wang

chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

Authors:Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut], Kai Wang [cre], Chris Lee [aut], Laura J. Scott [ths], Maureen A. Sartor [ths]

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chipenrich.pdf |chipenrich.html✨
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NEWS

# Install 'chipenrich' in R:
install.packages('chipenrich', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:chipenrich-2.29.0(bioc 3.20)chipenrich-2.28.0(bioc 3.19)

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

immunooncologychipseqepigeneticsfunctionalgenomicsgenesetenrichmenthistonemodificationregression

4.46 score 29 scripts 292 downloads 21 exports 149 dependencies

Last updated 25 days agofrom:ae52d559e7. Checks:OK: 1 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024

Exports:assign_peak_segmentsassign_peaksbroadenrichcalc_peak_gene_overlapchipenrichhybridenrichload_peaksnum_peaks_per_genepeaks2genesplot_chipenrich_splineplot_dist_to_tssplot_gene_coverageplot_polyenrich_splinepolyenrichproxRegread_bedsupported_genesetssupported_genomessupported_locusdefssupported_methodssupported_read_lengths

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemcheckmatechipenrich.dataclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydeldirdigestevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimemultcompmunsellmvtnormnlmennetopensslorg.Dm.eg.dborg.Dr.eg.dborg.Hs.eg.dborg.Mm.eg.dborg.Rn.eg.dbpillarpkgconfigplogrplyrpngpolsplineprettyunitsprogressquantregR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrrestfulrRhtslibrjsonrlangrmarkdownrmsrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssandwichsassscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsysTH.datatibbletidyselecttinytextzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLXVectoryamlzlibbioczoo

chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Ryan P. Welch, Chee Lee, Raymond G. Cavalcante, Chris Lee, Kai Wang, Laura J. Scott, Maureen A. Sartor

Rendered fromchipenrich-vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-06-03
Started: 2016-08-26

Readme and manuals

Help Manual

Help pageTopics
Assign whole peaks to all overlapping defined gene loci.assign_peak_segments
Assign peak midpoints to defined gene loci.assign_peaks
Run Broad-Enrich on broad genomic regionsbroadenrich
Add peak overlap and ratio to result of 'num_peaks_per_gene()'calc_peak_gene_overlap
Run ChIP-Enrich on narrow genomic regionschipenrich
chipenrich: Gene Set Enrichment For ChIP-seq Peak Data and Other Genomic Regionschipenrich_package
Function to filter genesets by locus definition and sizefilter_genesets
Get the correct organism code based on genomegenome_to_organism
Get Entrez ID to gene symbol mappings for custom locus definitionsgenome_to_orgdb
Get the test function name from the method nameget_test_method
Running Hybrid test, either from scratch or using two results fileshybridenrich
Convert a BEDX+Y data.frame and into GRangesload_peaks
Aggregate peak assignments over the 'gene_id' columnnum_peaks_per_gene
Run the test process up to, but not including the enrichment tests.peaks2genes
QC plot for ChIP-Enrichplot_chipenrich_spline
Plot histogram of distance from peak to nearest TSSplot_dist_to_tss
QC plot for Broad-Enrichplot_gene_coverage
QC plot for Poly-Enrichplot_polyenrich_spline
Run Poly-Enrich on narrow genomic regionspolyenrich
Post process the 'data.frame' of enrichment resultspost_process_enrichments
A helper function to post-process peak GRangespostprocess_peak_grs
Run Proximity Regulation test on a set of narrow genomic regionsproxReg
Read files containing peaks or genomic regionsread_bed
Function to read custom gene sets from fileread_geneset
Function to read custom locus definition from fileread_ldef
Function to read custom mappability filesread_mappa
Recode a vector of number of peaks to binary based on thresholdrecode_peaks
Reset n_cores for Windowsreset_ncores_for_windows
Function to setup genesetssetup_genesets
Function to setup locus definitionssetup_locusdef
Function to setup mappabilitysetup_mappa
Display supported genesets for gene set enrichment.supported_genesets
Display supported genomes.supported_genomes
Display supported locus definitionssupported_locusdefs
Display supported gene set enrichment methods.supported_methods
Display supported read lengths for mappabilitysupported_read_lengths