Package: chipenrich 2.37.0

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

# Install 'chipenrich' in R:

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

On BioConductor:chipenrich-2.37.0(bioc 3.24)chipenrich-2.36.0(bioc 3.23)

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

immunooncology chipseq epigenetics functionalgenomics genesetenrichment histonemodification regression

5.19 score 52 scripts 2 mentions 21 exports 148 dependencies

Last updated from:0fee2454ce. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	382
linux-devel-x86_64	WARNING	679
source / vignettes	OK	577
linux-release-x86_64	WARNING	707
macos-release-arm64	WARNING	525
macos-oldrel-arm64	WARNING	348
windows-devel	WARNING	832
windows-release	WARNING	800
windows-oldrel	WARNING	837
wasm-release	OK	380

Exports:assign_peak_segments assign_peaks broadenrich calc_peak_gene_overlap chipenrich hybridenrich load_peaks num_peaks_per_gene peaks2genes plot_chipenrich_spline plot_dist_to_tss plot_gene_coverage plot_polyenrich_spline polyenrich proxReg read_bed supported_genesets supported_genomes supported_locusdefs supported_methods supported_read_lengths

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem checkmate chipenrich.data cigarillo cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray deldir digest evaluate farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lifecycle magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime multcomp mvtnorm nlme nnet openssl org.Dm.eg.db org.Dr.eg.db org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db pillar pkgconfig plyr png polspline prettyunits progress quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr restfulr Rhtslib rjson rlang rmarkdown rms rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sandwich sass scales Seqinfo snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys TH.data tibble tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML XVector yaml zoo

chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Rendered fromchipenrich-vignette.Rmdusingknitr::rmarkdown

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

Help page	Topics
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 regions	broadenrich
Add peak overlap and ratio to result of 'num_peaks_per_gene()'	calc_peak_gene_overlap
Run ChIP-Enrich on narrow genomic regions	chipenrich
chipenrich: Gene Set Enrichment For ChIP-seq Peak Data and Other Genomic Regions	chipenrich_package
Function to filter genesets by locus definition and size	filter_genesets
Get the correct organism code based on genome	genome_to_organism
Get Entrez ID to gene symbol mappings for custom locus definitions	genome_to_orgdb
Get the test function name from the method name	get_test_method
Running Hybrid test, either from scratch or using two results files	hybridenrich
Convert a BEDX+Y data.frame and into GRanges	load_peaks
Aggregate peak assignments over the 'gene_id' column	num_peaks_per_gene
Run the test process up to, but not including the enrichment tests.	peaks2genes
QC plot for ChIP-Enrich	plot_chipenrich_spline
Plot histogram of distance from peak to nearest TSS	plot_dist_to_tss
QC plot for Broad-Enrich	plot_gene_coverage
QC plot for Poly-Enrich	plot_polyenrich_spline
Run Poly-Enrich on narrow genomic regions	polyenrich
Post process the 'data.frame' of enrichment results	post_process_enrichments
A helper function to post-process peak GRanges	postprocess_peak_grs
Run Proximity Regulation test on a set of narrow genomic regions	proxReg
Read files containing peaks or genomic regions	read_bed
Function to read custom gene sets from file	read_geneset
Function to read custom locus definition from file	read_ldef
Function to read custom mappability files	read_mappa
Recode a vector of number of peaks to binary based on threshold	recode_peaks
Reset n_cores for Windows	reset_ncores_for_windows
Function to setup genesets	setup_genesets
Function to setup locus definitions	setup_locusdef
Function to setup mappability	setup_mappa
Display supported genesets for gene set enrichment.	supported_genesets
Display supported genomes.	supported_genomes
Display supported locus definitions	supported_locusdefs
Display supported gene set enrichment methods.	supported_methods
Display supported read lengths for mappability	supported_read_lengths

Package: chipenrich 2.37.0

chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

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