{ "_id": "6abbb5f699f7aa8c6aa48791", "Package": "diffwrap", "Type": "Package", "Title": "Differential Expression Analysis of RNA-Seq Data", "Version": "0.6-3", "Date": "2026-08-10", "Authors@R": "person(list(\"Vidal\", \"Meeri\", \"Reija\", \"Bogdan\", \"Adrien\"), list(\"Fey\", \"Pekkarinen\", \"Hieta\", \"Iancu\", \"Janssens\"), email = list(\"vidal.fey@gmail.com\", \"meeri.pekkarinen@gmail.com\", \"reija.hieta@geneviatechnologies.com\", \"bogdan.iancu@abo.fi\", \"Adrien.RFM.Janssens@proton.me\"), role = list(c(\"aut\", \"cre\"), \"aut\", \"aut\", \"aut\", \"aut\"))", "Description": "Functions for differential expression analysis of read\ncounts from messenger RNA (mRNA) sequencing (RNA-Seq) data or\nmicro RNA (miRNA) expression values generated by the\nComprehensive Analysis Pipeline for microRNA Sequencing\n(CAP-miRSeq) 'expression_reports.sh' script. The workflow\nfollows the 'edgeR'-'limma' expression data analysis pipeline\nproviding options for different approaches, such as \"pure\"\n'edgeR', voom or paired samples. The functions in the package\ngenerate text files with differential expression lists,\noptionally annotated with information from 'biomart',\nexpression summary plots as well as several quality control\n(QC) plots. The main function, diffExpr(), is a convenience\nwrapper performing all steps automatically based on sensible\ndefaults. Methods are described in Robinson, McCarthy and Smyth\n(2010) , Ritchie et al.\n(2015) , Law et al. (2014)\n and Sun et al. (2014)\n.", "Maintainer": "Vidal Fey ", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "quarto", "NeedsCompilation": "no", "Author": "Vidal Fey [aut, cre], Meeri Pekkarinen [aut], Reija Hieta\n[aut], Bogdan Iancu [aut], Adrien Janssens [aut]", "Config/roxygen2/version": "8.0.0", "Packaged": { "Date": "2026-09-29 12:51:01 UTC", "User": "root" }, "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-08-30 13:00:50 UTC", "RemoteUrl": "https://github.com/cran/diffwrap", "RemoteRef": "HEAD", "RemoteSha": "27e8b17c4356ad19204cc427f71dbc2dd7b8033e", "_user": "cran", "_type": "src", "_file": "diffwrap_0.6-3.tar.gz", "_fileid": "https://r2.ropensci.org/60c9be9258c8fbaa71f7afd83d63e3d358d4c67e6a65cbb92d6776c0203646c4", "_filesize": 1046382, "_sha256": "60c9be9258c8fbaa71f7afd83d63e3d358d4c67e6a65cbb92d6776c0203646c4", "_expires": "2027-01-07T12:58:28.000Z", "_created": "2026-09-29T12:51:01.000Z", "_published": "2026-09-29T12:58:30.586Z", "_jobs": [ { "job": 109414559053, "time": 385, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11033614964" }, { "job": 109414559170, "time": 340, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "11034372108" }, { "job": 109412643737, "time": 297, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11034361079" }, { "job": 109414559178, "time": 206, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11033768390" }, { "job": 109414559129, "time": 288, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11033903410" }, { "job": 109414559085, "time": 277, "config": "windows-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "11035050323" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/36570347662", "_status": "success", "_upstream": "https://github.com/cran/diffwrap", "_commit": { "id": 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"Suggests" }, { "package": "scatterplot3d", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "WriteXLS", "role": "Suggests" }, { "package": "biomaRt", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-35", "n": 1 } ], "_tags": [ { "name": "0.6-3", "date": "2026-08-30" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 630, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 388, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/diffwrap" }, "_searchresults": 0, "_quarto": true, "_topics": [ "quarto" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/diffwrap.html", "extra/manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.6-3", "date": "2026-09-08" } ], "_exports": [ "%>%", "diff_expr_3d_scatterplot", "diff_expr_biomart", "diff_expr_dendro_plot", "diff_expr_extract_contrasts", "diff_expr_filter_counts", "diff_expr_fit", "diff_expr_get_samp_info", "diff_expr_ggplot_mds", "diff_expr_ma_plot", "diff_expr_make_contrasts", "diff_expr_make_design", "diff_expr_mds_plot", "diff_expr_PCA", "diff_expr_PCA_ggbiplot", "diff_expr_PCA_ggplot", "diff_expr_pseudo_counts", "diff_expr_pval_hist_plot", "diff_expr_QC_plots", "diff_expr_read_counts", "diff_expr_volcano_plot", "diffExpr", "diffr_expr_generate_cleaned_de_table_output", "diffr_pheatmap", "diffr_venn", "ggbiplot.n", "pheatmap_plots", "plot_enrichment_network", "prepare_scale_for_legend", "prepare_volcano_of_given_property", "run_clusterProfiler_GO", "run_clusterProfiler_KEGG", "run_gprofiler", "run.topGO", "runEnrichmentAnalyses" ], "_datasets": [ { "name": "diffwrap_counts", "title": "Simulated RNA-Seq read counts for the package examples", "object": "diffwrap_counts", "class": [ "matrix", "array" ], "fields": [ "S01", "S02", "S03", "S04", "S05", "S06", "S07", "S08" ], "rows": 405, "table": true, "tojson": true }, { "name": "diffwrap_samp_info", "title": "Sample sheet accompanying the simulated example counts", "object": "diffwrap_samp_info", "class": [ "data.frame" ], "fields": [ "SampleName", "Group", "Subject", "PlotName" ], "rows": 8, "table": true, "tojson": true } ], "_help": [ { "page": "correlogram_pheatmap", "title": "Function to create a correlogram pheatmap, i.e., a plot to check randomness in the data set.", "topics": [ "correlogram_pheatmap" ] }, { "page": "diff_expr_3d_scatterplot", "title": "Function to generate a 3D scatterplot", "topics": [ "diff_expr_3d_scatterplot" ] }, { "page": "diff_expr_biomart", "title": "Function to retrieve additional information from biomart", "topics": [ "diff_expr_biomart" ] }, { "page": "diff_expr_dendro_plot", "title": "Function to generate dendrogram plots based on hierarchical clustering", "topics": [ "diff_expr_dendro_plot" ] }, { "page": "diff_expr_extract_contrasts", "title": "Function to extract contrasts and generate top tables and plots", "topics": [ "diff_expr_extract_contrasts" ] }, { "page": "diff_expr_filter_counts", "title": "Function to filter counts", "topics": [ "diff_expr_filter_counts" ] }, { "page": "diff_expr_fit", "title": "Function to compute linear model fit and optionally apply 'voom' beforehand", "topics": [ "diff_expr_fit" ] }, { "page": "diff_expr_get_samp_info", "title": "Function to standardize samp.info sample information data frame", "topics": [ "diff_expr_get_samp_info" ] }, { "page": "diff_expr_ggplot_mds", "title": "Function to generate a MDS plot using `ggplot2`", "topics": [ "diff_expr_ggplot_mds" ] }, { "page": "diff_expr_ma_plot", "title": "Function to generate a M-A plot using `ggplot2`", "topics": [ "diff_expr_ma_plot" ] }, { "page": "diff_expr_make_contrasts", "title": "Function to make contrast matrix", "topics": [ "diff_expr_make_contrasts" ] }, { "page": "diff_expr_make_design", "title": "Function to create design matrix", "topics": [ "diff_expr_make_design" ] }, { "page": "diff_expr_mds_plot", "title": "Wrapper around `limma::plotMDS` to generate a MDS plot", "topics": [ "diff_expr_mds_plot" ] }, { "page": "diff_expr_PCA", "title": "Function to do PCA using `stats::prcomp`", "topics": [ "diff_expr_PCA" ] }, { "page": "diff_expr_PCA_ggbiplot", "title": "Function to generate a PCA biplot using `ggbiplot.n`, a version of `ggbiplot` from https://github.com/vqv/ggbiplot.", "topics": [ "diff_expr_PCA_ggbiplot" ] }, { "page": "diff_expr_PCA_ggplot", "title": "Function to generate an ordinary two-dimensional PCA plot using `ggplot2`", "topics": [ "diff_expr_PCA_ggplot" ] }, { "page": "diff_expr_pseudo_counts", "title": "Function to calculate pseudo counts representing batch-corrected normalised but untransformed values", "topics": [ "diff_expr_pseudo_counts" ] }, { "page": "diff_expr_pval_hist_plot", "title": "Function to generate a histogram of the P-Value distribution", "topics": [ "diff_expr_pval_hist_plot" ] }, { "page": "diff_expr_QC_plots", "title": "Main wrapper function for QC plots", "topics": [ "diff_expr_QC_plots" ] }, { "page": "diff_expr_read_counts", "title": "Function to read counts as produced by htseq-count", "topics": [ "diff_expr_read_counts" ] }, { "page": "diff_expr_volcano_plot", "title": "Function to generate a Volcano plot using `ggplot2`", "topics": [ "diff_expr_volcano_plot" ] }, { "page": "diffExpr", "title": "Main wrapper for executing the entire pipeline from reading in expression data such as count files to producing text files and graphs", "topics": [ "diffExpr" ] }, { "page": "diffr_expr_generate_cleaned_de_table_output", "title": "Helper function to generate an output table with only most relevant columns", "topics": [ "diffr_expr_generate_cleaned_de_table_output" ] }, { "page": "diffr_pheatmap", "title": "Function to create a heatmap from differential gene expression values", "topics": [ "diffr_pheatmap" ] }, { "page": "diffr_venn", "title": "Function to produce a Venn diagram of differentially expressed gene tables", "topics": [ "diffr_venn" ] }, { "page": "diffwrap", "title": "Differential expression analysis of RNA-Seq data", "concept": [ "RNA-seq", "differential gene expression", "edgeR", "limma", "linear modelling", "pathway analysis" ], "topics": [ "diffwrap" ] }, { "page": "diffwrap_counts", "title": "Simulated RNA-Seq read counts for the package examples", "topics": [ "diffwrap_counts" ] }, { "page": "diffwrap_samp_info", "title": "Sample sheet accompanying the simulated example counts", "topics": [ "diffwrap_samp_info" ] }, { "page": "format_ensembl_ids_annotated_to_term", "title": "Helper function for formatting the gene ID column of enrichment data frame.", "topics": [ "format_ensembl_ids_annotated_to_term" ] }, { "page": "get_hm_breaks", "title": "Function to define breaks to be used for changing the palette of the heatmap.", "topics": [ "get_hm_breaks" ] }, { "page": "get_hm_colors", "title": "Function to compute colour palettes to be used in the heatmap.", "topics": [ "get_hm_colors" ] }, { "page": "ggbiplot.n", "title": "Make a biplot of PCA output data using ggplot2.", "topics": [ "ggbiplot.n" ] }, { "page": "make_pheatmap_anno_color", "title": "Function to create the annotation colour list used in the heatmap", "topics": [ "make_pheatmap_anno_color" ] }, { "page": "pheatmap_plots", "title": "Function to generate heatmap of gene expression values", "topics": [ "pheatmap_plots" ] }, { "page": "plot_enrichment_network", "title": "Function for making network visualisation based on enrichment result, DE gene table and thresholding. Can take the input tables either as data frames or Excel files", "topics": [ "plot_enrichment_network" ] }, { "page": "prepare_scale_for_legend", "title": "Helper function for enrichment visualisations: prepare plot legend y coordinates and labels", "topics": [ "prepare_scale_for_legend" ] }, { "page": "prepare_volcano_of_given_property", "title": "Helper function that returns a volcano plot.", "topics": [ "prepare_volcano_of_given_property" ] }, { "page": "quantile_breaks", "title": "Function to define quantile breaks to be used for changing the palette of the heatmap.", "topics": [ "quantile_breaks" ] }, { "page": "reorderFactors", "title": "Function which reorders the levels of a column of a data frame specified as a factor", "topics": [ "reorderFactors" ] }, { "page": "run_clusterProfiler_GO", "title": "Runs clusterProfiler GO enrichment function for a DEG list or for a ranked gene list.", "topics": [ "run_clusterProfiler_GO" ] }, { "page": "run_clusterProfiler_KEGG", "title": "Runs clusterProfiler KEGG enrichment function for a DEG list or for a ranked gene list.", "topics": [ "run_clusterProfiler_KEGG" ] }, { "page": "run_gprofiler", "title": "Runs gprofiler function for a DEG list or for a ranked gene list.", "topics": [ "run_gprofiler" ] }, { "page": "run.topGO", "title": "Function to run GO term enrichment analysis using the 'topGO' package.", "topics": [ "run.topGO" ] }, { "page": "runEnrichmentAnalyses", "title": "Wrapper for executing various enrichment analyses", "topics": [ "runEnrichmentAnalyses" ] } ], "_rundeps": [ "admisc", "AnnotationDbi", "askpass", "assertthat", "backports", "base64enc", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "biomaRt", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "checkmate", "cli", "cluster", "colorspace", "convertid", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "digest", "dplyr", "edgeR", "evaluate", "expm", "farver", "fastmap", "filelock", "fontawesome", "foreign", 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