{ "_id": "6a1ad5cc1d7bb097a09e53ef", "Package": "dittoSeq", "Type": "Package", "Title": "User Friendly Single-Cell and Bulk RNA Sequencing Visualization", "Version": "1.25.0", "Authors@R": "c(person(\"Daniel\", \"Bunis\", email = \"daniel.bunis@ucsf.edu\", role=c(\"aut\", \"cre\")),\nperson(\"Jared\", \"Andrews\", email = \"jared.andrews07@gmail.com\", role=c(\"aut\", \"ctb\")))", "Description": "A universal, user friendly, single-cell and bulk RNA\nsequencing visualization toolkit that allows highly\ncustomizable creation of color blindness friendly,\npublication-quality figures. dittoSeq accepts both\nSingleCellExperiment (SCE) and Seurat objects, as well as the\nimport and usage, via conversion to an SCE, of\nSummarizedExperiment or DGEList bulk data. Visualizations\ninclude dimensionality reduction plots, heatmaps, scatterplots,\npercent composition or expression across groups, and more.\nCustomizations range from size and title adjustments to\nautomatic generation of annotations for heatmaps, overlay of\ntrajectory analysis onto any dimensionality reduciton plot,\nhidden data overlay upon cursor hovering via ggplotly\nconversion, and many more. All with simple, discrete inputs.\nColor blindness friendliness is powered by legend adjustments\n(enlarged keys), and by allowing the use of shapes or\nletter-overlay in addition to the carefully selected\ndittoColors().", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "biocViews": "Software, Visualization, RNASeq, SingleCell, GeneExpression,\nTranscriptomics, DataImport", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:51:58 UTC", "RemoteUrl": "https://github.com/bioc/dittoSeq", "RemoteRef": "HEAD", "RemoteSha": "ae7346c1c47ec90e0ca1c13dd42bda7b382817f3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:43:37 UTC", "User": "root" }, "Author": "Daniel Bunis [aut, cre],\nJared Andrews [aut, ctb]", "Maintainer": "Daniel Bunis ", "MD5sum": "22601d3d9083c6c240997950ac98b317", "_user": "bioc", "_type": "src", "_file": 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SingleCellExperiment object containing bulk or single-cell data", "topics": [ "addPrcomp" ] }, { "page": "Darken", "title": "Darkens input colors by a set amount", "topics": [ "Darken" ] }, { "page": "demux.calls.summary", "title": "Plots the number of annotations per sample, per lane", "topics": [ "demux.calls.summary" ] }, { "page": "demux.SNP.summary", "title": "Plots the number of SNPs sequenced per droplet", "topics": [ "demux.SNP.summary" ] }, { "page": "demuxlet.example", "title": "demuxlet.example", "topics": [ "demuxlet.example" ] }, { "page": "dittoBarPlot", "title": "Outputs a stacked bar plot to show the percent composition of samples, groups, clusters, or other groupings", "topics": [ "dittoBarPlot" ] }, { "page": "dittoColors", "title": "Extracts the dittoSeq default colors", "topics": [ "dittoColors" ] }, { "page": "dittoDimPlot", "title": "Shows data overlayed on a tsne, pca, or similar type of plot", "topics": [ "dittoDimPlot" ] }, { "page": "dittoDotPlot", "title": "Compact plotting of per group summaries for expression of multiple features", "topics": [ "dittoDotPlot" ] }, { "page": "dittoFreqPlot", "title": "Plot cell type/cluster/identity frequencies per sample and per grouping", "topics": [ "dittoFreqPlot" ] }, { "page": "dittoHeatmap", "title": "Outputs a heatmap of given genes", "topics": [ "dittoHeatmap" ] }, { "page": "dittoHex", "title": "Show RNAseq data, grouped into hexagonal bins, on a scatter or dimensionality reduction plot", "topics": [ "dittoDimHex", "dittoHex", "dittoScatterHex" ] }, { "page": "dittoPlot", "title": "Plots continuous data for customizeable cells'/samples' groupings on a y- (or x-) axis", "topics": [ "dittoBoxPlot", "dittoPlot", "dittoRidgeJitter", "dittoRidgePlot" ] }, { "page": "dittoPlotVarsAcrossGroups", "title": "Generates a dittoPlot where data points are genes/metadata summaries, per groups, instead of individual values per cells/samples.", "topics": [ "dittoPlotVarsAcrossGroups" ] }, { "page": "dittoScatterPlot", "title": "Show RNAseq data overlayed on a scatter plot", "topics": [ "dittoScatterPlot" ] }, { "page": "dittoSeq", "title": "dittoSeq", "topics": [ "dittoSeq-package", "dittoSeq" ] }, { "page": "gene", "title": "Returns the expression values of a gene for all cells/samples", "topics": [ "gene" ] }, { "page": "GeneTargeting", "title": "Control of Gene/Feature targeting", "topics": [ "GeneTargeting" ] }, { "page": "getGenes", "title": "Returns the names of all genes of a target object.", "topics": [ "getGenes" ] }, { "page": "getMetas", "title": "Returns the names of all meta.data slots of a target object.", "topics": [ "getMetas" ] }, { "page": "getReductions", "title": "Returns the names of all dimensionality reduction slots of a target object.", "topics": [ "getReductions" ] }, { "page": "importDemux", "title": "Extracts Demuxlet information into a pre-made SingleCellExperiment or Seurat object", "topics": [ "importDemux" ] }, { "page": "importDittoBulk", "title": "import bulk sequencing data into a SingleCellExperiment format that will work with other dittoSeq functions.", "topics": [ "importDittoBulk" ] }, { "page": "isBulk", "title": "Retrieve whether a given object would be treated as bulk versus single-cell by dittoSeq", "topics": [ "isBulk" ] }, { "page": "isGene", "title": "Tests if input is the name of a gene in a target object.", "topics": [ "isGene" ] }, { "page": "isMeta", "title": "Tests if an input is the name of a meta.data slot in a target object.", "topics": [ "isMeta" ] }, { "page": "Lighten", "title": "Lightens input colors by a set amount", "topics": [ "Lighten" ] }, { "page": "meta", "title": "Returns the values of a meta.data for all cells/samples", "topics": [ "meta" ] }, { "page": "metaLevels", "title": "Gives the distinct values of a meta.data slot (or ident)", "topics": [ "metaLevels" ] }, { "page": "multi_dittoDimPlot", "title": "Generates dittoDimPlots for multiple features.", "topics": [ "multi_dittoDimPlot" ] }, { "page": "multi_dittoDimPlotVaryCells", "title": "Generates multiple dittoDimPlots, for a single feature, where each showing different cells", "topics": [ "multi_dittoDimPlotVaryCells" ] }, { "page": "multi_dittoPlot", "title": "Generates dittoPlots for multiple features.", "topics": [ "multi_dittoPlot" ] }, { "page": "setBulk", "title": "Set whether a SingleCellExperiment object should be treated as bulk versus single-cell by dittoSeq", "topics": [ "setBulk", "setBulk,SingleCellExperiment-method" ] }, { "page": "Simulate", "title": "Simulates what a colorblind person would see for any dittoSeq plot!", "topics": [ "Simulate" ] } ], "_readme": "https://github.com/bioc/dittoSeq/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "colorspace", "cowplot", "cpp11", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "ggrepel", "ggridges", "glue", "gridExtra", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", 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