{ "_id": "6ac1a849773a0037682c010c", "Package": "hcocena", "Title": "Horizontal Integration and Analysis of Multiple Transcriptomics\nDatasets", "Version": "0.99.12", "Authors@R": "c(\nperson(given = \"Thomas\",\nfamily = \"Ulas\",\nrole = c(\"aut\", \"cre\"),\nemail = \"t.ulas@uni-bonn.de\",\ncomment = c(ORCID = \"0000-0002-9785-4197\")),\nperson(given = \"Waqar\",\nfamily = \"Hanif\",\nrole = c(\"ctb\")))", "Description": "Tools for the joint analysis of multiple transcriptomics\ndatasets using a network-based integration approach. The\npackage provides an S4 object model based on\nMultiAssayExperiment for reproducible analysis of single-layer\nand multi-layer studies. It includes workflows for clustering,\nmodule visualization, functional annotation, upstream\ninference, and longitudinal follow-up while retaining\ncompatibility helpers for legacy hCoCena objects.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "biocViews": "Software, Clustering, GeneExpression, KEGG, Network,\nNetworkInference, Transcriptomics, WorkflowStep", "BiocType": "Software", "URL": "https://github.com/BioCompNet/hcocena", "BugReports": "https://github.com/BioCompNet/hcocena/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl libx11-dev zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-10-03 21:41:46 UTC", "RemoteUrl": "https://github.com/BiocStaging/hcocena", "RemoteRef": "HEAD", "RemoteSha": "d0b918c0e0b390678cceba94ccaa9d2fc0ddd95d", "Packaged": { "Date": "2026-10-04 00:56:37 UTC", "User": "root" }, "Author": "Thomas Ulas [aut, cre] (ORCID: ),\nWaqar Hanif [ctb]", "Maintainer": "Thomas Ulas ", "_user": "biocstaging", "_type": "src", "_file": "hcocena_0.99.12.tar.gz", "_fileid": "https://r2.ropensci.org/c45497166ba67700cc0f1fdcaf1908d7a9081b35dd3bdd379745be1c4ff4de4e", "_filesize": 2242419, "_sha256": "c45497166ba67700cc0f1fdcaf1908d7a9081b35dd3bdd379745be1c4ff4de4e", "_expires": "2027-01-12T01:13:43.000Z", "_created": "2026-10-04T00:56:37.000Z", "_published": "2026-10-04T01:13:45.681Z", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37166146258", "_status": "success", "_upstream": "https://github.com/BiocStaging/hcocena", "_commit": { "id": "d0b918c0e0b390678cceba94ccaa9d2fc0ddd95d", "author": "Thomas Ulas ", "committer": "Thomas Ulas ", "message": "0.99.12: one LLM interface, rebuilt upstream inference, redrawn knowledge network\n\n- hc_llm_enrichment() / hc_llm_import() replace the old LLM functions; one\n interface for Claude, OpenAI, Gemini, local vLLM and a no-API-key route\n through the web chat. Four plots from separate requests: general processes\n (features only), contextual state and key regulators (with context), and\n processes grounded on enrichment terms (optionally upstream regulators and\n DoRAG literature).\n- hc_plot_llm_enrichment(): no gene lists in the plot, at most two lines,\n square heatmap cells, Greek letters spelled out.\n- hc_upstream_inference(): modules and regulators linked by over-representation\n against the network genes with BH over all tests (calibrated on random\n modules); per-condition activity from decoupleR ULM over all network genes;\n regulation sign, consistency, TF-in-module, redundancy; CollecTRI with\n DoRothEA fallback; PROGENy top 100 genes per pathway.\n- hc_plot_enrichment_upstream_network(): heatmap | upstream regulators ->\n modules -> enriched terms with square cells, regulator effect colours,\n redundant terms collapsed and term links on the module pages.\n- gridExtra and gtable dropped from Imports.\n\nCo-Authored-By: Claude Opus 5.5 \n", "time": 1791063706 }, "_maintainer": { "name": "Thomas Ulas", "email": "t.ulas@uni-bonn.de", "login": "ulas-lab", "description": "Leading the bioinformatics side at the LIMES and at PRECISE. 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