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Package: ArchR 1.0.3

Ryan Corces

ArchR: Analyzing single-cell regulatory chromatin in R.

This package is designed to streamline scATAC analyses in R.

Authors:Jeffrey Granja [aut], Ryan Corces [aut, cre], Paulina Paiz [aut], Immanuel Abdi [aut, ctb]

ArchR_1.0.3.tar.gz
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ArchR.pdf |ArchR.html✨
ArchR/json (API)

# Install 'ArchR' in R:

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

Bug tracker:https://github.com/greenleaflab/archr/issues

Pkgdown site:https://www.archrproject.com

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

7.94 score 398 stars 2.4k scripts 164 exports 264 dependencies

Last updated 22 days agofrom:6feec354ad. Checks:1 OK, 9 ERROR. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 18 2025
R-4.5-win-x86_64	ERROR	Feb 18 2025
R-4.5-mac-x86_64	ERROR	Feb 18 2025
R-4.5-mac-aarch64	ERROR	Feb 18 2025
R-4.5-linux-x86_64	ERROR	Feb 18 2025
R-4.4-win-x86_64	ERROR	Feb 18 2025
R-4.4-mac-x86_64	ERROR	Feb 18 2025
R-4.4-mac-aarch64	ERROR	Feb 18 2025
R-4.3-win-x86_64	ERROR	Feb 18 2025
R-4.3-mac-x86_64	ERROR	Feb 18 2025

Exports:.DollarNames.ArchRProject %bcin%%bcni%%ni%addArchRAnnotations addArchRChrPrefix addArchRDebugging addArchRGenome addArchRH5Level addArchRLocking addArchRLogging addArchRThreads addArchRVerbose addBgdPeaks addCellColData addClusters addCoAccessibility addCombinedDims addDemuxletResults addDeviationsMatrix addDoubletScores addFeatureCounts addFeatureMatrix addGeneExpressionMatrix addGeneIntegrationMatrix addGeneScoreMatrix addGroupCoverages addHarmony addImputeWeights addIterativeLSI addModuleScore addMonocleTrajectory addMotifAnnotations addPeak2GeneLinks addPeakAnnotations addPeakMatrix addPeakSet addProjectSummary addReproduciblePeakSet addSampleColData addSlingShotTrajectories addTileMatrix addTrajectory addTSNE addUMAP ArchRBrowser ArchRBrowserTrack ArchRHeatmap ArchRPalettes ArchRProject confusionMatrix correlateMatrices correlateTrajectories createArrowFiles createGeneAnnotation createGenomeAnnotation createLogFile customEnrichment enrichHeatmap exportGroupSE exportPeakMatrixForSTREAM extendGR filterChrGR filterDoublets findMacs2 getArchRChrPrefix getArchRDebugging getArchRGenome getArchRH5Level getArchRLogging getArchRThreads getArchRVerbose getArrowFiles getAvailableMatrices getBgdPeaks getBlacklist getCellColData getCellNames getChromLengths getChromSizes getCoAccessibility getEmbedding getExons getFeatures getFootprints getFragmentsFromArrow getFragmentsFromProject getGeneAnnotation getGenes getGenome getGenomeAnnotation getGroupBW getGroupFragments getGroupSE getGroupSummary getImputeWeights getInputFiles getMarkerFeatures getMarkers getMatches getMatrixFromArrow getMatrixFromProject getMonocleTrajectories getOutputDirectory getPBGroupSE getPeak2GeneLinks getPeakAnnotation getPeakSet getPositions getProjectSummary getReducedDims getSampleColData getSampleNames getSeqnames getTestArrow getTestFragments getTestProject getTrajectory getTSS getTutorialData getValidBarcodes getVarDeviations ggAlignPlots ggGroup ggHex ggOneToOne ggPoint import10xFeatureMatrix imputeMatrix installExtraPackages loadArchRProject mapLabels markerFeatures markerHeatmap markerPlot nCells nonOverlappingGR paletteContinuous paletteDiscrete peak2GeneHeatmap peakAnnoEnrichment plotBrowserTrack plotEmbedding plotEnrichHeatmap plotFootprints plotFragmentSizes plotGroups plotMarkerHeatmap plotMarkers plotPDF plotPeak2GeneHeatmap plotTrajectory plotTrajectoryHeatmap plotTSSEnrichment projectBulkATAC recoverArchRProject reformatFragmentFiles saveArchRProject setArchRLocking subsetArchRProject subsetCells theme_ArchR trajectoryHeatmap validBSgenome

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob brew brio BSgenome bslib cachem callr caTools chromVAR chromVARmotifs circlize cli clipr clue cluster CNEr codetools colorspace commonmark ComplexHeatmap cowplot cpp11 crayon credentials crosstalk curl data.table DBI DelayedArray deldir desc devtools diffobj digest DirichletMultinomial doParallel dotCall64 downlit dplyr dqrng DT ellipsis evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges gert GetoptLong ggplot2 ggrepel ggridges gh gitcreds GlobalOptions globals glue GO.db goftest gplots gridExtra gtable gtools harmony here highr hms htmltools htmlwidgets httpuv httr httr2 ica igraph ini IRanges irlba isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leidenbase lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI motifmatchr munsell nabor nlme openssl parallelly patchwork pbapply pillar pkgbuild pkgconfig pkgdown pkgload plogr plotly plyr png polyclip poweRlaw pracma praise presto prettyunits processx profvis progress progressr promises ps purrr pwalign R.methodsS3 R.oo R.utils R6 ragg RANN rappdirs rcmdcheck RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML RCurl readr remotes reshape2 restfulr reticulate rhdf5 rhdf5filters Rhdf5lib RhpcBLASctl Rhtslib rjson rlang rmarkdown ROCR roxygen2 rprojroot Rsamtools RSpectra RSQLite rstudioapi rtracklayer Rtsne rversions S4Arrays S4Vectors sass scales scattermore sctransform seqLogo sessioninfo Seurat SeuratObject shape shiny sitmo snow sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys systemfonts tensor testthat textshaping TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils urlchecker usethis utf8 uwot vctrs viridisLite vroom waldo whisker withr xfun XML xml2 xopen xtable XVector yaml zip zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Accessing cellColData directly from dollar.sign accessor	.DollarNames.ArchRProject
This function allows you to suppress specific warnings and was originally created by Antoine Fabri ("Moody_Mudskipper"): see https://stackoverflow.com/a/55182432/697473 Sometimes R throws warning messages that we don't want to see. The base 'suppressWarnings()' function permits one to suppress warnings, but it is tricky to selectively suppress only certain warnings on the basis of a regular expression or another condition. This function allows one to do that.	.suppressSpecificWarnings
Subset cells directly from ArchRProject	[.ArchRProject
Generic matching function for S4Vector objects	%bcin%
Negated matching function for S4Vector objects	%bcni%
Negated Value Matching	%ni%
Accessing cellColData directly from dollar.sign accessor	$.ArchRProject
Add directly to cellColData directly from dollar.sign accessor	$<-.ArchRProject
Add ArchR annotations to an ArchRProject	addArchRAnnotations
Add a globally-applied requirement for chromosome prefix	addArchRChrPrefix
Set ArchR Debugging	addArchRDebugging
Add a globally defined genome to all ArchR functions.	addArchRGenome
Add a globally-applied compression level for h5 files	addArchRH5Level
Add a globally-applied H5 file locking setup	addArchRLocking
Set ArchR Logging	addArchRLogging
Add a globally-applied number of threads to use for parallel computing.	addArchRThreads
Set ArchR Verbosity for Log Messaging	addArchRVerbose
Add Background Peaks to an ArchRProject	addBgdPeaks
Add information to cellColData in an ArchRProject	addCellColData
Add cluster information to an ArchRProject	addClusters
Add Peak Co-Accessibility to an ArchRProject	addCoAccessibility
Combine two or more modalities dimensionality reductions.	addCombinedDims
Add Demuxlet Results to ArchR Project	addDemuxletResults
Add a matrix of deviations for a given peakAnnotation to Arrow Files in ArchRProject	addDeviationsMatrix
Add Doublet Scores to a collection of ArrowFiles or an ArchRProject	addDoubletScores
This function will add total counts of scATAC cells in provided features into ArchRProject.	addFeatureCounts
Add a feature matrix to an ArchRProject or a set of ArrowFiles	addFeatureMatrix
Add Gene Expression Matrix to ArrowFiles or an ArchRProject	addGeneExpressionMatrix
Add a GeneIntegrationMatrix to ArrowFiles or an ArchRProject	addGeneIntegrationMatrix
Add GeneScoreMatrix to ArrowFiles or an ArchRProject	addGeneScoreMatrix
Add Group Coverages to an ArchRProject object	addGroupCoverages
Add Harmony Batch Corrected Reduced Dims to an ArchRProject	addHarmony
Add Imputation Weights to an ArchRProject	addImputeWeights
Add an Iterative LSI-based dimensionality reduction to an ArchRProject	addIterativeLSI
Add Module Scores to an ArchRProject	addModuleScore
Add a Monocle Trajectory to an ArchR Project	addMonocleTrajectory
Add motif annotations to an ArchRProject	addMotifAnnotations
Add Peak2GeneLinks to an ArchRProject	addPeak2GeneLinks
Add peak annotations to an ArchRProject	addPeakAnnotations
Add a Peak Matrix to the ArrowFiles of an ArchRProject	addPeakMatrix
Add a peak set to an ArchRProject	addPeakSet
Add projectSummary to an ArchRProject	addProjectSummary
Add a Reproducible Peak Set to an ArchRProject	addReproduciblePeakSet
Add information to sampleColData in an ArchRProject	addSampleColData
Add a Slingshot Trajectories to an ArchR Project	addSlingShotTrajectories
Add TileMatrix to ArrowFiles or an ArchRProject	addTileMatrix
Add a Supervised Trajectory to an ArchR Project	addTrajectory
Add a TSNE embedding of a reduced dimensions object to an ArchRProject	addTSNE
Add a UMAP embedding of a reduced dimensions object to an ArchRProject	addUMAP
Launch ArchR Genome Browser	ArchRBrowser
Plot Nice Lookng Heatmap Using Complex Heatmap	ArchRHeatmap
List of color palettes that can be used in plots	ArchRPalettes
Create ArchRProject from ArrowFiles	ArchRProject
Create a Confusion Matrix based on two value vectors	confusionMatrix
Correlate Matrices within an ArchRProject	correlateMatrices
Correlate Trajectories	correlateTrajectories
Create Arrow Files	createArrowFiles
Create a gene annotation object for ArchR	createGeneAnnotation
Create a genome annotation object for ArchR	createGenomeAnnotation
Create a Log File for ArchR	createLogFile
Hypergeometric Enrichment in input peak ranges.	customEnrichment
Get a PeakMatrix stored in an ArchRProject and write out for STREAM	exportPeakMatrixForSTREAM
Extend regions from a Genomic Ranges object	extendGR
Filters unwanted seqlevels from a Genomic Ranges object or similar object	filterChrGR
Filter Doublets From an ArchRProject	filterDoublets
Find the installed location of the MACS2 executable	findMacs2
Get a globally-applied requirement for chromosome prefix	getArchRChrPrefix
Get ArchR Debugging	getArchRDebugging
Get the globally defined genome, the geneAnnotation, or genomeAnnotation objects associated with the globally defined genome.	getArchRGenome
Get globally-applied compression level for h5 files	getArchRH5Level
Get ArchR Logging	getArchRLogging
Get globally-applied number of threads to use for parallel computing.	getArchRThreads
Set ArchR Verbosity for Log Messaging	getArchRVerbose
Get ArrowFiles from an ArchRProject	getArrowFiles
Get a list available matrices in the ArrowFiles storted in an ArchRProject	getAvailableMatrices
Get Background Peaks from an ArchRProject	getBgdPeaks
Get the blacklist from an ArchRProject	getBlacklist
Get cellColData from an ArchRProject	getCellColData
Get cellNames from an ArchRProject	getCellNames
Get chromLengths from ArchRProject	getChromLengths
Get chromSizes from ArchRProject	getChromSizes
Get the peak co-accessibility from an ArchRProject	getCoAccessibility
Get embedding information stored in an ArchRProject	getEmbedding
Get the exons from an ArchRProject	getExons
Get the features that could be selected from a given data matrix within an ArchRProject	getFeatures
Calculate footprints from an ArchRProject	getFootprints
Get the fragments from an ArrowFile	getFragmentsFromArrow
Get the fragments from an ArchRProject	getFragmentsFromProject
Get geneAnnotation from an ArchRProject	getGeneAnnotation
Get the genes from an ArchRProject	getGenes
Get the genome used by an ArchRProject	getGenome
Get the genomeAnnotation from an ArchRProject	getGenomeAnnotation
Export Group BigWigs	getGroupBW
Export Group Fragment Files	getGroupFragments
Export Group Summarized Experiment	getGroupSE
Get summary for Groups in ArchRProject	getGroupSummary
Get Imputation Weights from ArchRProject	getImputeWeights
Get Input Files from paths to create arrows	getInputFiles
Identify Marker Features for each cell grouping	getMarkerFeatures
Get Marker Features from a marker summarized experiment	getMarkers
Get peak annotation matches from an ArchRProject	getMatches
Get a data matrix stored in an ArrowFile	getMatrixFromArrow
Get a data matrix stored in an ArchRProject	getMatrixFromProject
Get a Monocle CDS of Trajectories that can be added to an ArchRProject	getMonocleTrajectories
Get outputDirectory from an ArchRProject	getOutputDirectory
Export PseudoBulk Group Summarized Experiment	getPBGroupSE
Get the peak-to-gene links from an ArchRProject	getPeak2GeneLinks
Get peakAnnotation from an ArchRProject	getPeakAnnotation
Get the peak set from an ArchRProject	getPeakSet
Get peak annotation positions from an ArchRProject	getPositions
Get projectSummary from an ArchRProject	getProjectSummary
Get dimensionality reduction information stored in an ArchRProject	getReducedDims
Get sampleColData from an ArchRProject	getSampleColData
Get the sample names from an ArchRProject	getSampleNames
Get the seqnames that could be selected from a given data matrix within an ArchRProject	getSeqnames
Get PBMC Small Test Arrow file	getTestArrow
Get PBMC Small Test Fragments	getTestFragments
Get PBMC Small Test Project	getTestProject
Get Supervised Trajectory from an ArchR Project	getTrajectory
Get the transcription start sites of all genes in an ArchRProject	getTSS
Get Relevant Data For ArchR Tutorials	getTutorialData
Get Valid Barcodes from 10x Cell Ranger output to pre-filter barcodes	getValidBarcodes
Get Variable Deviations across cells in ArchRProject.	getVarDeviations
Align ggplot plots vertically or horizontally	ggAlignPlots
A ggplot-based ridge/violin plot wrapper function	ggGroup
A ggplot-based Hexplot wrapper function summary of points in a standardized manner	ggHex
A ggplot-based one-to-one dot plot wrapper function	ggOneToOne
A ggplot-based dot plot wrapper function	ggPoint
Import Feature Matrix from 10x Feature HDF5 file.	import10xFeatureMatrix
Impute a matrix with impute weights	imputeMatrix
Install extra packages used in ArchR that are not installed by default	installExtraPackages
Load Previous ArchRProject into R	loadArchRProject
Re-map a character vector of labels from an old set of labels to a new set of labels	mapLabels
Get the number of cells from an ArchRProject/ArrowFile	nCells
Retreive a non-overlapping set of regions from a Genomic Ranges object	nonOverlappingGR
Continuous Color Palette	paletteContinuous
Optimized discrete color palette generation	paletteDiscrete
Peak Annotation Hypergeometric Enrichment in Marker Peaks.	peakAnnoEnrichment
Plot an ArchR Region Track	plotBrowserTrack
Visualize an Embedding from ArchR Project	plotEmbedding
Plot a Heatmap of Peak Annotation Hypergeometric Enrichment in Marker Peaks.	plotEnrichHeatmap
Plot Footprints	plotFootprints
Plot the fragment size distribution for each sample	plotFragmentSizes
Visualize Groups from ArchR Project	plotGroups
Plot a Heatmap of Identified Marker Features	plotMarkerHeatmap
Plot Differential Markers	plotMarkers
Plot PDF in outputDirectory of an ArchRProject	plotPDF
Plot Peak2Gene Heatmap from an ArchRProject	plotPeak2GeneHeatmap
Visualize a Trajectory from ArchR Project	plotTrajectory
Plot a Heatmap of Features across a Trajectory	plotTrajectoryHeatmap
Plot a TSS Enrichment Plot for Each Sample	plotTSSEnrichment
Project Bulk ATAC-seq data into single cell subspace	projectBulkATAC
Recover ArchRProject if broken sampleColData/cellColData	recoverArchRProject
Reformat Fragment Files to be Tabix and Chr Sorted	reformatFragmentFiles
Save ArchRProject for Later Usage	saveArchRProject
Set a globally-applied H5 file locking setup	setArchRLocking
Subset an ArchRProject for downstream analysis	subsetArchRProject
Subset cells in an ArchRProject.	subsetCells
ggplot2 default theme for ArchR	theme_ArchR
Get/Validate BSgenome	validBSgenome