Package: chromVAR 1.27.0

Alicia Schep

chromVAR: Chromatin Variation Across Regions

Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.

Authors:Alicia Schep [aut, cre], Jason Buenrostro [ctb], Caleb Lareau [ctb], William Greenleaf [ths], Stanford University [cph]

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chromVAR.pdf |chromVAR.html✨
chromVAR/json (API)
NEWS

# Install 'chromVAR' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

example_counts - Example_counts
mini_counts - Mini_counts
mini_dev - Mini_dev
mini_ix - Mini_ix

On BioConductor:chromVAR-1.27.0(bioc 3.20)chromVAR-1.26.0(bioc 3.19)

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

singlecell sequencing generegulation immunooncology

44 exports 7.72 score 152 dependencies 1 dependents 46 mentions 708 scripts 2.5k downloads

Last updated 5 months agofrom:641df9dc6c. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 22 2024
R-4.5-win-x86_64	NOTE	Sep 22 2024
R-4.5-linux-x86_64	NOTE	Sep 22 2024
R-4.4-win-x86_64	NOTE	Sep 22 2024
R-4.4-mac-x86_64	NOTE	Sep 22 2024
R-4.4-mac-aarch64	NOTE	Sep 22 2024
R-4.3-win-x86_64	NOTE	Sep 22 2024
R-4.3-mac-x86_64	NOTE	Sep 22 2024
R-4.3-mac-aarch64	NOTE	Sep 22 2024

Exports:addGCBias annotationMatches annotationMatches<-assembleKmers cbind chromVAR_theme computeDeviations computeExpectations computeVariability counts counts<-deviations deviationScores deviationsCovariability deviationsTsne differentialDeviations differentialVariability filterPeaks filterSamples filterSamplesPlot getAnnotationCorrelation getAnnotations getAnnotationSynergy getBackgroundPeaks getCisGroups getCounts getFragmentsPerPeak getFragmentsPerSample getJasparMotifs getPeaks getPermutedData getSampleCorrelation getSampleDepths getSampleDistance getTotalFragments makeBiasBins makePermutedSets matchKmers plotDeviationsTsne plotKmerMismatch plotVariability pwmDistance rbind readNarrowpeaks

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib cachem caTools cli clipr CNEr codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI DelayedArray digest DirichletMultinomial dplyr DT evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue GO.db gtable gtools highr hms htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nabor nlme openssl pillar pkgconfig plogr plotly plyr png poweRlaw pracma prettyunits progress promises purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer Rtsne S4Arrays S4Vectors sass scales seqLogo shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xtable XVector yaml zlibbioc

chromVAR

Alicia Schep

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Sep 22 2024.

Last update: 2017-10-16
Started: 2017-02-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
addGCBias	addGCBias addGCBias,RangedSummarizedExperiment-method addGCBias,SummarizedExperiment-method
annotationMatches	annoation_matches<-,SummarizedExperiment-method annotationMatches annotationMatches,SummarizedExperiment-method annotationMatches<- annotationMatches<-,SummarizedExperiment-method
assembleKmers	assembleKmers
cbind method for chromVARDeviations	cbind,chromVARDeviations-method
chromVAR: A package for computing variability across sets of peaks.	chromVAR-package chromVAR
chromVAR_theme	chromVAR_theme
chromVARDeviations	chromVARDeviations-class
computeDeviations	computeDeviations computeDeviations,MatrixOrmatrix,list-method computeDeviations,MatrixOrmatrix,MatrixOrmatrix-method computeDeviations,MatrixOrmatrix,missingOrNULL-method computeDeviations,MatrixOrmatrix,SummarizedExperiment-method computeDeviations,SummarizedExperiment,list-method computeDeviations,SummarizedExperiment,MatrixOrmatrix-method computeDeviations,SummarizedExperiment,missingOrNULL-method computeDeviations,SummarizedExperiment,SummarizedExperiment-method
computeExpectations	computeExpectations computeExpectations,MatrixOrmatrix-method computeExpectations,SummarizedExperiment-method
computeVariability	computeVariability
Accessors for the 'counts' slot of a SummarizedExperiment	counts,SummarizedExperiment-method counts<-,SummarizedExperiment,MatrixOrmatrix-method counts<-,SummarizedExperiment-method
deviations	deviations deviations,chromVARDeviations-method
deviationScores	deviationScores deviationScores,chromVARDeviations-method
deviationsCovariability	deviationsCovariability
deviationsTsne	deviationsTsne
differentialDeviations	differentialDeviations
differentialVariability	differentialVariability
example_counts	example_counts
filterPeaks	filterPeaks
filterSamples	filterSamples
filterSamplesPlot	filterSamplesPlot
getAnnotationCorrelation	getAnnotationCorrelation getAnnotationCorrelation,MatrixOrmatrix,list-method getAnnotationCorrelation,MatrixOrmatrix,MatrixOrmatrix-method getAnnotationCorrelation,MatrixOrmatrix,SummarizedExperiment-method getAnnotationCorrelation,SummarizedExperiment,list-method getAnnotationCorrelation,SummarizedExperiment,MatrixOrmatrix-method getAnnotationCorrelation,SummarizedExperiment,SummarizedExperiment-method
getAnnotations	getAnnotations getAnnotations,character-method getAnnotations,data.frame-method getAnnotations,GRangesList-method getAnnotations,list-method getAnnotations,MatrixOrmatrix-method
getAnnotationSynergy	getAnnotationSynergy getAnnotationSynergy,MatrixOrmatrix,list-method getAnnotationSynergy,MatrixOrmatrix,MatrixOrmatrix-method getAnnotationSynergy,MatrixOrmatrix,SummarizedExperiment-method getAnnotationSynergy,SummarizedExperiment,list-method getAnnotationSynergy,SummarizedExperiment,MatrixOrmatrix-method getAnnotationSynergy,SummarizedExperiment,SummarizedExperiment-method
getBackgroundPeaks	getBackgroundPeaks getBackgroundPeaks,MatrixOrmatrix-method getBackgroundPeaks,RangedSummarizedExperiment-method getBackgroundPeaks,SummarizedExperiment-method
getCisGroups	getCisGroups getCisGroups,GenomicRanges-method getCisGroups,RangedSummarizedExperiment-method
getCounts	getCounts
getFragmentsPerPeak	getFragmentsPerPeak getFragmentsPerPeak,MatrixOrmatrix-method getFragmentsPerPeak,SummarizedExperiment-method
getFragmentsPerSample	getFragmentsPerSample getFragmentsPerSample,MatrixOrmatrix-method getFragmentsPerSample,SummarizedExperiment-method
getJasparMotifs	getJasparMotifs
getPeaks	getPeaks
getPermutedData	getPermutedData
getSampleCorrelation	getSampleCorrelation
getSampleDepths	getSampleDepths
getSampleDistance	getSampleDistance
getTotalFragments	getTotalFragments getTotalFragments,MatrixOrmatrix-method getTotalFragments,SummarizedExperiment-method
makeBiasBins	makeBiasBins makeBiasBins,MatrixOrmatrix-method makeBiasBins,RangedSummarizedExperiment-method makeBiasBins,SummarizedExperiment-method
makePermutedSets	makePermutedSets makePermutedSets,MatrixOrmatrix,list-method makePermutedSets,MatrixOrmatrix,MatrixOrmatrix-method makePermutedSets,MatrixOrmatrix,SummarizedExperiment-method makePermutedSets,RangedSummarizedExperiment,list-method makePermutedSets,RangedSummarizedExperiment,MatrixOrmatrix-method makePermutedSets,RangedSummarizedExperiment,SummarizedExperiment-method makePermutedSets,SummarizedExperiment,list-method makePermutedSets,SummarizedExperiment,MatrixOrmatrix-method makePermutedSets,SummarizedExperiment,SummarizedExperiment-method
matchKmers	matchKmers matchKmers,character,character-method matchKmers,character,DNAString-method matchKmers,character,DNAStringSet-method matchKmers,character,GenomicRanges-method matchKmers,character,RangedSummarizedExperiment-method matchKmers,DNAString,ANY-method matchKmers,DNAStringSet,ANY-method matchKmers,numeric,ANY-method
mini_counts	mini_counts
mini_dev	mini_dev
mini_ix	mini_ix
plotDeviationsTsne	plotDeviationsTsne
plotKmerMismatch	plotKmerMismatch
plotVariability	plotVariability
pwmDistance	pwmDistance
rbind method chromVARDeviations	rbind,chromVARDeviations-method
readNarrowpeaks	readNarrowpeaks