Package: compEpiTools 1.39.0

Mattia Furlan

compEpiTools: Tools for computational epigenomics

Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.

Authors:Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre]

compEpiTools_1.39.0.tar.gz
compEpiTools_1.39.0.zip(r-4.5)compEpiTools_1.39.0.zip(r-4.4)compEpiTools_1.39.0.zip(r-4.3)
compEpiTools_1.39.0.tgz(r-4.4-any)compEpiTools_1.39.0.tgz(r-4.3-any)
compEpiTools_1.39.0.tar.gz(r-4.5-noble)compEpiTools_1.39.0.tar.gz(r-4.4-noble)
compEpiTools_1.39.0.tgz(r-4.4-emscripten)compEpiTools_1.39.0.tgz(r-4.3-emscripten)
compEpiTools.pdf |compEpiTools.html✨
compEpiTools/json (API)
NEWS

# Install 'compEpiTools' in R:

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

On BioConductor:compEpiTools-1.39.0(bioc 3.20)compEpiTools-1.38.0(bioc 3.19)

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

bioconductor-package

31 exports 1.00 score 159 dependencies 10 mentions

Last updated 2 months agofrom:8c7ce3c987

Exports:countOverlapsInBins distanceFromTSS enhancers featuresLength findLncRNA getPromoterClass GR2fasta GRanges2ucsc GRangesInPromoters GRannotate GRannotateSimple GRbaseCoverage GRcoverage GRcoverageInbins GRcoverageSummit GRenrichment GRmidpoint GRsetwidth heatmapData heatmapPlot makeGtfFromDb matchEnhancers overlapOfGRanges palette2d plotStallingIndex simplifyGOterms stallingIndex topGOres TSS ucsc2GRanges unionMaxScore

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem caTools checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue GO.db gplots graph gridExtra gtable gtools Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma magrittr marray MASS Matrix MatrixGenerics matrixStats memoise methylPipe mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray SparseM statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex topGO UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

compEpiTools

Rendered fromcompEpiTools.rnwusingknitr::knitron Jun 17 2024.

Last update: 2015-06-08
Started: 2014-08-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for computational epigenomics	compEpiTools-package compEpiTools
given a query and a subject GRanges returns a matrix of counts of subject in bins of query	countOverlapsInBins countOverlapsInBins,GRanges-method countOverlapsInBins-methods
Returns the GRanges annotated with info about the closer TSS	distanceFromTSS distanceFromTSS,GRanges-method distanceFromTSS-methods
A GRanges method to define enhancers based on H3K4me1 peaks	enhancers enhancers,GRanges-method enhancers-methods
Identify putative long non coding RNAs (lncRNA)	findLncRNA
Determining the CpG promoter class and the average CpG content	getPromoterClass getPromoterClass,TxDb-method getPromoterClass-methods
A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome	GR2fasta GR2fasta,GRanges-method GR2fasta-methods
A GRanges method to convert ranges information into UCSC format	GRanges2ucsc GRanges2ucsc,GRanges-method GRanges2ucsc-methods
Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters	GRangesInPromoters GRangesInPromoters,GRanges-method GRangesInPromoters-methods
Based on a GRanges and a TxDb, returns the GRanges with a series of annotations	GRannotate GRannotate,GRanges-method GRannotate-methods
a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic	GRannotateSimple GRannotateSimple,GRanges-method GRannotateSimple-methods
Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range	GRbaseCoverage GRbaseCoverage,GRanges-method GRbaseCoverage-methods
based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.	GRcoverage GRcoverage,GRanges-method GRcoverage-methods GRcoverageInbins GRcoverageInbins,GRanges-method GRcoverageInbins-methods
Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range	GRcoverageSummit GRcoverageSummit,GRanges-method GRcoverageSummit-methods
Determines the enrichment over a set of genomic regions given two BAM files	GRenrichment GRenrichment,GRanges-method GRenrichment-methods
Returns a GRanges containing the mid point of a GRanges	GRmidpoint GRmidpoint,GRanges-method GRmidpoint-methods
Set the width of a GRanges based on the mid point of each region	GRsetwidth GRsetwidth,GRanges-method GRsetwidth-methods
Based on a list of GRanges, determine various kind of counts before displaying a heatmap	heatmapData
displays the heatmap based on the data from heatmapData	heatmapPlot
Utilities to transform a TxDb into a GTF file	featuresLength featuresLength,TxDb-method featuresLength-methods makeGtfFromDb makeGtfFromDb,TxDb-method makeGtfFromDb-methods
GRanges method to match enhancers with putative targets sites	matchEnhancers matchEnhancers,GRanges-method matchEnhancers-methods
visualization of GRanges overlap	overlapOfGRanges overlapOfGRanges,GRanges-method overlapOfGRanges-methods
build a two dimensional color palette	palette2d
Stalling Index plots	plotStallingIndex
simplify a list of GO terms	simplifyGOterms
returns a list with average read count on TSS, gene body, and stalling index for a number of samples	stallingIndex
determines GeneOntology (GO) enriched terms for a set of Entrez gene ids	topGOres
based on a TxDb returns a GRanges with the TSS positions for all transcripts	TSS
Convert UCSC-formatted genomic positions into a GRanges	ucsc2GRanges
GRanges method to perform union of peaks keeping the score of the most significant peak	unionMaxScore unionMaxScore,GRanges-method unionMaxScore-methods