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GenomicFeatures methods utils stats tools httr rjson DBI RSQLite IRanges UCSC.utils AnnotationDbi Biobase BiocIO rtracklayer biomaRt multiHiCcompare: data.table dplyr HiCcompare edgeR BiocParallel qqman pheatmap methods GenomicRanges graphics stats utils pbapply GenomeInfoDbData GenomeInfoDb aggregation bluster: stats methods utils cluster Matrix Rcpp igraph S4Vectors BiocParallel BiocNeighbors assorthead clustree: ggraph checkmate igraph dplyr grid ggplot2 viridis methods rlang tidygraph ggrepel RcppArmadillo: Rcpp stats utils methods xml2: cli methods rlang beeswarm: stats graphics grDevices utils Cairo: grDevices graphics ggthemes: ggplot2 graphics grid lifecycle methods purrr scales stringr tibble scRNAseq: SingleCellExperiment utils methods Matrix BiocGenerics S4Vectors SparseArray DelayedArray GenomicRanges SummarizedExperiment ExperimentHub AnnotationHub AnnotationDbi ensembldb GenomicFeatures alabaster.base alabaster.matrix alabaster.sce gypsum jsonlite DBI RSQLite prettyunits: RcppML: Rcpp Matrix methods stats RcppEigen origami: abind methods data.table assertthat future future.apply listenv isoband: grid utils shinyAce: shiny jsonlite utils tools jquerylib: htmltools BiocNeighbors: Rcpp methods assorthead dichromat: stats TrajectoryUtils: SingleCellExperiment methods stats Matrix igraph S4Vectors SummarizedExperiment rhdf5filters: Rhdf5lib circlize: graphics GlobalOptions shape grDevices utils stats colorspace methods grid VariantAnnotation: methods BiocGenerics MatrixGenerics GenomeInfoDb GenomicRanges SummarizedExperiment Rsamtools utils DBI Biobase S4Vectors IRanges XVector Biostrings AnnotationDbi rtracklayer BSgenome GenomicFeatures Rhtslib rappdirs: SingleCellExperiment: SummarizedExperiment methods utils stats S4Vectors BiocGenerics GenomicRanges DelayedArray crosstalk: htmltools jsonlite lazyeval R6 rmarkdown: bslib evaluate fontawesome htmltools jquerylib jsonlite knitr methods tinytex tools utils xfun yaml SingleR: SummarizedExperiment methods Matrix S4Vectors DelayedArray DelayedMatrixStats BiocParallel BiocNeighbors stats utils Rcpp beachmat assorthead codetools: curl: rematch: graphlayouts: igraph Rcpp RcppArmadillo gridExtra: gtable grid grDevices graphics utils rtracklayer: methods GenomicRanges XML BiocGenerics S4Vectors IRanges XVector GenomeInfoDb Biostrings curl httr Rsamtools GenomicAlignments BiocIO tools restfulr BiocBookDemo: ontologyIndex: ProtGenerics: methods parallel: tools compiler rpart: graphics stats grDevices xfun: grDevices stats tools DEoptimR: stats tidyselect: cli glue lifecycle rlang vctrs withr