{ "_id": "6a19560aacfb0bcc41de1c04", "Package": "InterCellar", "Title": "InterCellar: an R-Shiny app for interactive analysis and\nexploration of cell-cell communication in single-cell\ntranscriptomics", "Version": "2.18.0", "Authors@R": "person('Marta', 'Interlandi', email = 'marta.interlandi01@gmail.com', role = c('cre', 'aut'), comment = c(ORCID = \"0000-0002-6863-2552\") )", "Description": "InterCellar is implemented as an R/Bioconductor Package\ncontaining a Shiny app that allows users to interactively\nanalyze cell-cell communication from scRNA-seq data. Starting\nfrom precomputed ligand-receptor interactions, InterCellar\nprovides filtering options, annotations and multiple\nvisualizations to explore clusters, genes and functions.\nFinally, based on functional annotation from Gene Ontology and\npathway databases, InterCellar implements data-driven analyses\nto investigate cell-cell communication in one or multiple\nconditions.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "Config/testthat/edition": "3", "URL": "https://github.com/martaint/InterCellar", "BugReports": "https://github.com/martaint/InterCellar/issues", "VignetteBuilder": "knitr", "biocViews": "Software, SingleCell, Visualization, GO, Transcriptomics", "PackageStatus": "Deprecated", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl python3 zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:55:15 UTC", "RemoteUrl": "https://github.com/bioc/InterCellar", "RemoteRef": "RELEASE_3_23", "RemoteSha": "12f9c0602a959c0e338b16dd3adb128ee7924a60", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:47:21 UTC", "User": "root" }, "Author": "Marta Interlandi [cre, aut] (ORCID:\n)", "Maintainer": "Marta Interlandi ", "MD5sum": "b0688ff65998889a6d5fba9424c27bdc", "_user": "bioc-release", "_type": "src", "_file": "InterCellar_2.18.0.tar.gz", "_fileid": "bf965eda4990715840da6ef01279987b0499140d0c7602215c40a6d2043957a8", "_filesize": 4081164, "_sha256": "bf965eda4990715840da6ef01279987b0499140d0c7602215c40a6d2043957a8", "_created": "2026-05-29T07:47:21.000Z", "_published": "2026-05-29T09:02:02.799Z", "_jobs": [ { "job": 78459884162, "time": 197, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7285789531" }, { "job": 78459884177, "time": 328, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7285826979" }, { "job": 78459884183, "time": 330, "config": 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"extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/martaint/intercellar", "_realowner": "bioc", "_cranurl": false, "_exports": [ "checkLL_RR", "getClusterNames", "getGeneTable", "getIntFlow", "run_app" ], "_datasets": [ { "name": "input.data", "title": "Input Data example", "object": "input.data", "file": "input.data.rda", "class": [ "data.table", "data.frame" ], "fields": [ "int_pair", "geneA", "geneB", "typeA", "typeB", "clustA", "clustB", "score", "p_value", "annotation_strategy", "int.type" ], "rows": 5638, "table": true, "tojson": true } ], "_help": [ { "page": "annotateGO", "title": "Perform GO annotation of input data", "topics": [ "annotateGO" ] }, { "page": "annotatePathways", "title": "Annotate pathways for input data", "topics": [ "annotatePathways" ] }, { "page": "buildPairsbyFunctionMatrix", "title": "Build binary matrix with int-pairs in rows, functions in cols", "topics": [ "buildPairsbyFunctionMatrix" ] }, { "page": "checkLL_RR", "title": "Manually change the annotation of L-L and R-R pairs", "topics": [ "checkLL_RR" ] }, { "page": "circlePlot", "title": "Plot circle plot", "topics": [ "circlePlot" ] }, { "page": "combineAnnotations", "title": "Combine GO annotation and pathways in a unique object", "topics": [ "combineAnnotations" ] }, { "page": "createBarPlot_CV", "title": "Create Barplot cluster-verse", "topics": [ "createBarPlot_CV" ] }, { "page": "createBarPlot1_ggplot", "title": "Create ggplot barplot to be saved in tiff", "topics": [ "createBarPlot1_ggplot" ] }, { "page": "createBarPlot2_CV", "title": "Create barplot of number of interaction for selected cluster", "topics": [ "createBarPlot2_CV" ] }, { "page": "createBarPlot2_ggplot", "title": "Create ggplot barplot of Nint per cluster selected", "topics": [ "createBarPlot2_ggplot" ] }, { "page": "createNetwork", "title": "Create Network of clusters", "topics": [ "createNetwork" ] }, { "page": "dendroIntPairModules", "title": "Get dendrogram of int pair modules", "topics": [ "dendroIntPairModules" ] }, { "page": "elbowPoint", "title": "Determine the elbow point on a curve (from package akmedoids)", "topics": [ "elbowPoint" ] }, { "page": "ensemblLink", "title": "Get html link to ensembl", "topics": [ "ensemblLink" ] }, { "page": "getBack2BackBarplot", "title": "Get back-to-back barplot for 2 conditions comparison", "topics": [ "getBack2BackBarplot" ] }, { "page": "getBarplotDF", "title": "Get dataframe for plotting barplot (all clusters)", "topics": [ "getBarplotDF" ] }, { "page": "getBarplotDF2", "title": "Get dataframe for barplot (by cluster)", "topics": [ "getBarplotDF2" ] }, { "page": "getClusterA_Names", "title": "Get cluster names only from sender cluster A", "topics": [ "getClusterA_Names" ] }, { "page": "getClusterColors", "title": "Get colors for clusters", "topics": [ "getClusterColors" ] }, { "page": "getClusterNames", "title": "Get clusters names from initial input data", "topics": [ "getClusterNames" ] }, { "page": "getClusterNetwork", "title": "Creating edges dataframe for network of clusters", "topics": [ "getClusterNetwork" ] }, { "page": "getClusterSize", "title": "Get Clusters size", "topics": [ "getClusterSize" ] }, { "page": "getDistinctCouplets", "title": "Get table of unique int-pairs/clust-pairs couplets", "topics": [ "getDistinctCouplets" ] }, { "page": "getDotPlot_selInt", "title": "Functions to plot DotPlots", "topics": [ "getDotPlot_selInt" ] }, { "page": "getGeneTable", "title": "Get table for gene-verse", "topics": [ "getGeneTable" ] }, { "page": "getGObiomaRt", "title": "Connection to Ensembl via biomaRt to get GO terms", "topics": [ "getGObiomaRt" ] }, { "page": "getHitsf", "title": "Subfunction to calculate significant functions by permutation test", "topics": [ "getHitsf" ] }, { "page": "getIntFlow", "title": "Get subset of interactions corresponding to a certain viewpoint and flow", "topics": [ "getIntFlow" ] }, { "page": "getNtermsBYdb", "title": "Calculate number of terms of a database", "topics": [ "getNtermsBYdb" ] }, { "page": "getNumLR", "title": "Get number of unique ligands and receptors", "topics": [ "getNumLR" ] }, { "page": "getPieChart", "title": "Get Pie Chart of unique couplets", "topics": [ "getPieChart" ] }, { "page": "getRadar_df", "title": "#' Get radar plot of relative numbers of interactions for a certain cell type #' #' @param tab_c1 barplot dataframe from Viewpoint generated by getBarplotDF2() containing data for condition 1 #' @param tab_c2 barplot dataframe from Viewpoint generated by getBarplotDF2() containing data for condition 2 #' @param tab_c3 barplot dataframe from Viewpoint generated by getBarplotDF2() containing data for condition 3 #' @param lab_c1 label for condition 1 #' @param lab_c2 label for condition 2 #' @param lab_c3 label for condition 3 #' @param cell_name label of cell type of interest #' #' @return plot #' @importFrom fmsb radarchart #' @importFrom data.table transpose getRadarPlot <- function(tab_c1, tab_c2, tab_c3, lab_c1, lab_c2, lab_c3, cell_name) if(is.null(tab_c3)) df <- merge(tab_c1, tab_c2, by = \"Clusters\", all = TRUE) colnames(df) <- c(\"Clusters\", \"nint_c1\", \"nint_c2\") else df <- merge(tab_c1, tab_c2, by = \"Clusters\", all = TRUE) df <- merge(df, tab_c3, by = \"Clusters\", all = TRUE) colnames(df) <- c(\"Clusters\", \"nint_c1\", \"nint_c2\", \"nint_c3\") df[is.na(df)] <- 0 cluster_names <- df$Clusters # add max and min max_nint <- max(df[, -1]) df <- add_column(df, max_nint, .after = \"Clusters\") df <- add_column(df, \"min_nint\" = 0, .after = \"max_nint\") radar_df <- data.table::transpose(df[, -1]) if(is.null(lab_c3)) rownames(radar_df) <- c(\"max\", \"min\", lab_c1, lab_c2) else rownames(radar_df) <- c(\"max\", \"min\", lab_c1, lab_c2, lab_c3) colnames(radar_df) <- cluster_names color <- c(\"#438ECC\", \"#E97778\", \"#00BA38\") fmsb::radarchart( radar_df, axistype = 1, # Customize the polygon pcol = color, pfcol = scales::alpha(color, 0.5), plwd = 2, plty = 1, # Customize the grid cglcol = \"grey\", cglty = 1, cglwd = 0.8, # Customize the axis axislabcol = \"grey30\", # Variable labels vlcex = 1.2, vlabels = colnames(radar_df), caxislabels = round(seq(from = 0, to = radar_df[\"max\",1], length.out = 5)), title = cell_name ) legend( x = \"bottomleft\", legend = rownames(radar_df[-c(1,2),]), horiz = FALSE, bty = \"n\", pch = 20 , col = color, text.col = \"black\", cex = 1, pt.cex = 1.5 ) Get radar df of relative numbers of interactions for a certain cell type", "topics": [ "getRadar_df" ] }, { "page": "getRankedTerms", "title": "Get table with ranked functional terms", "topics": [ "getRankedTerms" ] }, { "page": "getSignif_table", "title": "Wrapper for other functions to get significant table of func terms", "topics": [ "getSignif_table" ] }, { "page": "getSignificantFunctions", "title": "Calculate significant function per intpair module", "topics": [ "getSignificantFunctions" ] }, { "page": "getSignificantFunctions_multiCond", "title": "Get significance of functional terms related to unique int-pairs per condition", "topics": [ "getSignificantFunctions_multiCond" ] }, { "page": "getSunburst", "title": "Get Sunburst plot of selected functional terms", "topics": [ "getSunburst" ] }, { "page": "getUMAPipModules", "title": "Get UMAP for IP modules", "topics": [ "getUMAPipModules" ] }, { "page": "getUniqueDotplot", "title": "Plot dotplot containing only unique int-pair/cluster pairs with many conditions", "topics": [ "getUniqueDotplot" ] }, { "page": "getUniqueIntpairs_byCond", "title": "Get table of unique int-pairs by condition", "topics": [ "getUniqueIntpairs_byCond" ] }, { "page": "goLink", "title": "Get GO link", "topics": [ "goLink" ] }, { "page": "input.data", "title": "Input Data example", "topics": [ "input.data" ] }, { "page": "read.cellchat", "title": "Read dataframe of cell-cell communication from CellChat (ligand/receptor)", "topics": [ "read.cellchat" ] 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"topics": [ "uniprotLink" ] }, { "page": "updateInputLR", "title": "Function that orders all interaction pairs as L-R. 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