Package: regioneR 1.39.0

Bernat Gel

regioneR: Association analysis of genomic regions based on permutation tests

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

Authors:Anna Diez-Villanueva <[email protected]>, Roberto Malinverni <[email protected]> and Bernat Gel <[email protected]>

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regioneR.pdf |regioneR.html✨
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NEWS

# Install 'regioneR' in R:

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

On BioConductor:regioneR-1.39.0(bioc 3.21)regioneR-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.

genetics chipseq dnaseq methylseq copynumbervariation

8.97 score 21 packages 2.7k scripts 2.8k downloads 30 mentions 34 exports 54 dependencies

Last updated 23 days agofrom:0c8711ef09. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:characterToBSGenome circularRandomizeRegions commonRegions createFunctionsList createRandomRegions emptyCacheRegioneR extendRegions filterChromosomes getChromosomesByOrganism getGenome getGenomeAndMask getMask joinRegions listChrTypes localZScore maskFromBSGenome meanDistance meanInRegions mergeRegions numOverlaps overlapGraphicalSummary overlapPermTest overlapRegions permTest plotRegions randomizeRegions recomputePermTest resampleGenome resampleRegions splitRegions subtractRegions toDataframe toGRanges uniqueRegions

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

regioneR: Association analysis of genomic regions based on permutation tests

Bernat Gel ([email protected]), Anna Diez-Villanueva ([email protected]) and Roberto Malinverni ([email protected])

Rendered fromregioneR.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2018-08-13

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Readme and manuals

Help Manual

Help page	Topics
characterToBSGenome	characterToBSGenome
Circular Randomize Regions	circularRandomizeRegions
Common Regions	commonRegions
Create Functions List	createFunctionsList
Create Random Regions	createRandomRegions
Empty Cache regioneR	emptyCacheRegioneR
Extend Regions	extendRegions
filterChromosomes	filterChromosomes
getChromosomesByOrganism	getChromosomesByOrganism
getGenome	getGenome
getGenomeAndMask	getGenomeAndMask
getMask	getMask
Join Regions	joinRegions
filterChromosomes listChrTypes	listChrTypes
Local z-score	localZScore
maskFromBSGenome	maskFromBSGenome
Mean Distance	meanDistance
Mean In Regions	meanInRegions
Merge Regions	mergeRegions
Number Of Overlaps	numOverlaps
Overlap Graphical Summary	overlapGraphicalSummary
Permutation Test for Overlap	overlapPermTest
Overlap Regions	overlapRegions
Permutation Test	permTest
Plot localZscore results	plot.localZScoreResults
Function for plotting the results from a 'permTestResults' object.	plot.permTestResults
Function for plotting the results from a 'permTestResultsList' object when more than one evaluation function was used.	plot.permTestResultsList
Plot Regions	plotRegions
Randomize Regions	randomizeRegions
Recompute Permutation Test	recomputePermTest
resampleGenome	resampleGenome
Resample Regions	resampleRegions
Split Regions	splitRegions
Subtract Regions	subtractRegions
toDataframe	toDataframe
toGRanges	toGRanges
Unique Regions	uniqueRegions

Package: regioneR 1.39.0

regioneR: Association analysis of genomic regions based on permutation tests

regioneR: Association analysis of genomic regions based on permutation tests

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)