{ "_id": "6a5f88d714e95619b75d69d7", "Package": "DgeaHeatmap", "Title": "Implementation of Functions to Analyze Nanostring and Other Data\nfor DGE and to Generate Heatmaps", "Version": "0.99.0", "Authors@R": "c(\nperson(\"Leonie Johanna\", \"Lancelle\",\nemail = \"leonie.lancelle@uni-bielefeld.de\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0004-3138-0752\"))\n)", "Description": "Package for data extraction from Nanostring GeoMx DSP\ndata, also works for other data. Simple functions for\nDifferential Expression Analysis. User-friendly and highly\ncustomizable functions for heatmap generation.", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "biocViews": "Bayesian,Clustering, DifferentialExpression, GeneExpression,\nNormalization, PrincipalComponent, RNASeq, Regression,\nSequencing, Software, Transcription, AlternativeSplicing,\nBatchEffect,BiomedicalInformatics, CellBiology,\nCheminformatics, DataImport, DifferentialSplicing, Epigenetics,\nExonArray, FunctionalGenomics, GeneSetEnrichment, Genetics,\nImmunoOncology, Metabolomics, MicroRNAArray, Microarray,\nMultipleComparison, OneChannel, Preprocessing,\nProprietaryPlatforms, Proteomics, QualityControl,\nSystemsBiology, TimeCourse, TwoChannel, mRNAMicroarray", "URL": "https://gitlab.ub.uni-bielefeld.de/spittaulab/Dgea_Heatmap_Package", "BugReports": "https://gitlab.ub.uni-bielefeld.de/spittaulab/Dgea_Heatmap_Package/-/issues", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev make libicu-dev libpng-dev libuv1-dev\nlibssl-dev perl zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-07-20 09:37:47 UTC", "RemoteUrl": "https://github.com/BiocStaging/DgeaHeatmap", "RemoteRef": "HEAD", "RemoteSha": "65a509be682ef287f8d7158d8a9555e8ad95e845", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-21 14:46:37 UTC", "User": "root" }, "Author": "Leonie Johanna Lancelle [aut, cre] (ORCID:\n)", "Maintainer": "Leonie Johanna Lancelle ", "_user": "biocstaging", "_type": "src", "_file": "DgeaHeatmap_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/34a69d4b98c37525bcea4b1f05599e2271c5d23929951fbfd5f93546eadd63ac", "_filesize": 2323883, "_sha256": "34a69d4b98c37525bcea4b1f05599e2271c5d23929951fbfd5f93546eadd63ac", "_expires": "2026-10-29T14:57:26.000Z", "_created": "2026-07-21T14:46:37.000Z", "_published": "2026-07-21T14:57:27.957Z", "_bioccheck": { "error": 0, "warning": 1, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293", "_status": "failure", "_upstream": "https://github.com/BiocStaging/DgeaHeatmap", "_commit": { "id": "65a509be682ef287f8d7158d8a9555e8ad95e845", "author": "Lancelle ", "committer": "Lancelle ", "message": "chore: remove untracked local config files from repository\n", "time": 1784540267 }, "_maintainer": { "name": "Leonie Johanna Lancelle", "email": "leonie.lancelle@uni-bielefeld.de", "login": "leolanci", "description": "\n", "uuid": 136694688, "orcid": "0009-0004-3138-0752" }, "_distro": "resolute", "_jobs": [ { "job": 88668748044, "time": 231, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8499356506" }, { "job": 88668747890, "time": 474, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8499490067" }, { "job": 88668747969, "time": 471, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8499488984" }, { "job": 88668748009, "time": 545, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8499564853" }, { "job": 88668747876, "time": 365, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8499460052" }, { "job": 88667415774, "time": 278, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8499223302" }, { "job": 88668747944, "time": 220, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8499350895" }, { "job": 88668748047, "time": 486, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8499496952" }, { "job": 88668748304, "time": 459, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8499483264" }, { "job": 88668748021, "time": 468, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8499488419" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "NanoStringNCTools", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "GeomxTools", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "EnvStats", "role": "Suggests" }, { "package": "GeoMxWorkflows", "role": "Suggests" }, { "package": "VennDiagram", "role": "Suggests" }, { "package": "ggiraph", "role": "Suggests" }, { "package": "stringr", "role": "Suggests" }, { "package": "ggvenn", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 8 }, { "week": "2025-31", "n": 7 }, { "week": "2025-32", "n": 5 }, { "week": "2026-05", "n": 5 }, { "week": "2026-07", "n": 11 }, { "week": "2026-08", "n": 7 }, { "week": "2026-09", "n": 2 }, { "week": "2026-11", "n": 2 }, { "week": "2026-12", "n": 1 }, { "week": "2026-14", "n": 2 }, { "week": "2026-15", "n": 2 }, { "week": "2026-21", "n": 1 }, { "week": "2026-25", "n": 1 }, { "week": "2026-30", "n": 2 } ], "_tags": [], "_topics": [ "bayesian", "clustering", "differentialexpression", "geneexpression", "normalization", "principalcomponent", "rnaseq", "regression", "sequencing", "software", "transcription", "alternativesplicing", "batcheffect", "biomedicalinformatics", "cellbiology", "cheminformatics", "dataimport", "differentialsplicing", "epigenetics", "exonarray", "functionalgenomics", "genesetenrichment", "genetics", "immunooncology", "metabolomics", "micrornaarray", "microarray", "multiplecomparison", "onechannel", "preprocessing", "proprietaryplatforms", "proteomics", "qualitycontrol", "systemsbiology", "timecourse", "twochannel", "mrnamicroarray" ], "_stars": 0, "_contributors": [ { "user": "leolanci", "count": 216, "uuid": 136694688 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 1 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DgeaHeatmap" }, "_devurl": "https://github.com/biocstaging/dgeaheatmap", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DgeaHeatmap.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_demoElem", "adv_Heatmap", "aExprsDataQC", "build_matrix", "color_setting", "column_clustering", "create_contrast_matrix_edgeR", "DGEADESeq2", "DGEAedgeR", "DGEALimma", "draw_adv_heatmap", "elbow_plot", "extract_genes_direction", "extractDEGenes", "filtering_for_top_exprGenes", "function_complexHeatmap_var", "genRawReadCountTable", "get_dist", "get_heatmap_colors", "individual_matrix", "Kmean_generation", "most_variable_genes", "pairwise_contrasts", "performing_kMeans", "prepare_dge_list", "print_heatmap", "row_clustering", "scale_counts", "set_annotation", "set_row_annotation", "set_sample_annotation", "show_data_distribution", "split_data_by_column", "summarise_bio_replicates", "summarize_edgeR_DEA" ], "_help": [ { "page": "add_demoElem", "title": "Build a matrix from an input csv file, with one column as rownames", "topics": [ "add_demoElem" ] }, { "page": "adv_Heatmap", "title": "Creating a color scheme based on the available color palettes of RColorBrewer for the heatmap.", "topics": [ "adv_Heatmap" ] }, { "page": "aExprsDataQC", "title": "Function for automatized quality control.", "topics": [ "aExprsDataQC" ] }, { "page": "build_matrix", "title": "Builds a matrix from an input csv file, with one column as rownames", "topics": [ "build_matrix" ] }, { "page": "color_setting", "title": "Function to set color scheme for a heatmap.", "topics": [ "color_setting" ] }, { "page": "column_clustering", "title": "Setting the column clustering", "topics": [ "column_clustering" ] }, { "page": "create_contrast_matrix_edgeR", "title": "create_contrast_matrix_edgeR", "topics": [ "create_contrast_matrix_edgeR" ] }, { "page": "DGEADESeq2", "title": "DGEADESeq2", "topics": [ "DGEADESeq2" ] }, { "page": "DGEAedgeR", "title": "DGEAedgeR", "topics": [ "DGEAedgeR" ] }, { "page": "DGEALimma", "title": "DGEALimma", "topics": [ "DGEALimma" ] }, { "page": "draw_adv_heatmap", "title": "Draw the advanced heatmap", "topics": [ "draw_adv_heatmap" ] }, { "page": "elbow_plot", "title": "Function to create an elbow plot to choose k for clustering by k-Means.", "topics": [ "elbow_plot" ] }, { "page": "extract_genes_direction", "title": "Get list of genes and their direction of regulation", "topics": [ "extract_genes_direction" ] }, { "page": "extractDEGenes", "title": "extractDEGenes", "topics": [ "extractDEGenes" ] }, { "page": "filtering_for_top_exprGenes", "title": "Function to filter a matrix to extract a chosen number of most variable rows through calculation of the variance.", "topics": [ "filtering_for_top_exprGenes" ] }, { "page": "function_complexHeatmap_var", "title": "Creating a heatmap with annotation of x most variable rows(genes).", "topics": [ "function_complexHeatmap_var" ] }, { "page": "genRawReadCountTable", "title": "Function to generating a raw read count table.", "topics": [ "genRawReadCountTable" ] }, { "page": "get_dist", "title": "Calculates the distance matrix", "topics": [ "get_dist" ] }, { "page": "get_heatmap_colors", "title": "Creating a color scheme based on the available color palettes of RColorBrewer for the heatmap.", "topics": [ "get_heatmap_colors" ] }, { "page": "individual_matrix", "title": "Creates a matrix only containing chosen columns of an original matrix with more data.", "topics": [ "individual_matrix" ] }, { "page": "Kmean_generation", "title": "Generates K-means for the columns and rows of a matrix.", "topics": [ "Kmean_generation" ] }, { "page": "most_variable_genes", "title": "Function to determine the most variable genes of each cluster to enable annotation..", "topics": [ "most_variable_genes" ] }, { "page": "pairwise_contrasts", "title": "Create pairwise contrasts", "topics": [ "pairwise_contrasts" ] }, { "page": "performing_kMeans", "title": "Function to perform k-Means clustering for a matrix and setting split to split a heatmap into clusters.", "topics": [ "performing_kMeans" ] }, { "page": "prepare_dge_list", "title": "DGEAedgeR", "topics": [ "prepare_dge_list" ] }, { "page": "print_heatmap", "title": "Function to build a heatmap using other functions.", "topics": [ "print_heatmap" ] }, { "page": "row_clustering", "title": "Setting the row clustering", "topics": [ "row_clustering" ] }, { "page": "scale_counts", "title": "Function to Z-count scale the values of a matrix.", "topics": [ "scale_counts" ] }, { "page": "set_annotation", "title": "Function to set row annotation for a heatmap.", "topics": [ "set_annotation" ] }, { "page": "set_row_annotation", "title": "Setting the row annotation", "topics": [ "set_row_annotation" ] }, { "page": "set_sample_annotation", "title": "Setting the sample annotation", "topics": [ "set_sample_annotation" ] }, { "page": "show_data_distribution", "title": "Function to visualize the data distribution within the data of a matrix.", "topics": [ "show_data_distribution" ] }, { "page": "split_data_by_column", "title": "Splitting data by group column with feature, pheno or protocol data to then get the mean.", "topics": [ "split_data_by_column" ] }, { "page": "summarise_bio_replicates", "title": "Summarizes columns biological replicates of a matrix into one.", "topics": [ "summarise_bio_replicates" ] }, { "page": "summarize_edgeR_DEA", "title": "Summarize the results of the DEA with edgeR", "topics": [ "summarize_edgeR_DEA" ] } ], "_readme": "https://github.com/BiocStaging/DgeaHeatmap/raw/HEAD/README.md", "_rundeps": [ "abind", "base64enc", "beeswarm", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "boot", "bslib", "cachem", "cellranger", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "data.table", "DelayedArray", "DESeq2", "digest", "doParallel", "dotCall64", "dplyr", "edgeR", "EnvStats", "evaluate", "farver", "fastmap", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "forcats", "foreach", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "gdtools", "generics", "GenomicRanges", "GeomxTools", "GetoptLong", "GGally", "ggbeeswarm", "ggiraph", "ggplot2", "ggstats", "ggthemes", "GlobalOptions", "globals", "glue", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "listenv", "lme4", "lmerTest", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "minqa", "NanoStringNCTools", "nlme", "nloptr", "nortest", "numDeriv", "parallelly", "patchwork", "pheatmap", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "progressr", "purrr", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "readxl", "reformulas", "rematch", "reshape2", "rjson", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "SeuratObject", "shape", "snow", "sp", "spam", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "systemfonts", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "vipor", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_score": 2.845098040014257, "_indexed": true, "_nocasepkg": "dgeaheatmap", "_universes": [ "biocstaging", "leolanci" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.0", "date": "2026-07-21T14:50:23.000Z", "distro": "resolute", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/32b32f753ee7d7fc35870e1c5868438d1671f0bbd65a6e6b0917163174a48c13", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" }, { "r": "4.6.1", "os": "linux", "version": "0.99.0", "date": "2026-07-21T14:50:22.000Z", "distro": "resolute", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/6c01a438a3ae6b2e500484fc27190a7dfaa1fd447dea01942be77b044871a173", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" }, { "r": "4.5.3", "os": "mac", "version": "0.99.0", "date": "2026-07-21T14:51:03.000Z", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/f899ebff5b3959b8e7abaded72cf6237a650b948f124711b902d706354a58140", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" }, { "r": "4.6.1", "os": "mac", "version": "0.99.0", "date": "2026-07-21T14:49:16.000Z", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/7c2ab978b392cb5929a1561dbed090576fd3ae8cb9fd842ab71d2b717198b0f2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.0", "date": "2026-07-21T14:50:33.000Z", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/858649b587f0013d686621041da1dcf783fb70c1a9d0b83db01dc4bc3e5e2314", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" }, { "r": "4.7.0", "os": "win", "version": "0.99.0", "date": "2026-07-21T14:49:26.000Z", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/46f5e10c0eab7aedb07d1a35fff9b28225a09b6e717a87fdc569e41931133cf7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" }, { "r": "4.5.3", "os": "win", "version": "0.99.0", "date": "2026-07-21T14:49:15.000Z", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/c5d30cfa402ae56884c677b4abf4d08ab331a8e243b431551334d469cf25297b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" }, { "r": "4.6.1", "os": "win", "version": "0.99.0", "date": "2026-07-21T14:49:01.000Z", "commit": "65a509be682ef287f8d7158d8a9555e8ad95e845", "fileid": "https://r2.ropensci.org/c91388e0e5f463bd41b18dc702814384f21a84c694905affc6ae8dfa472c8b04", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29840348293" } ] }