https://biocstaging.r-universe.devRecent package updates in biocstagingR-universehttps://github.com/biocstaging.pnghttps://biocstaging.r-universe.devMon, 01 Jun 2026 12:18:51 GMThelena@crowell.eu (Helena L. Crowell)R interface to Python/scverse's 'spatialdata' framework for unified spatial omics data handling. Adheres to OME-NGFF standards, providing lazy, on-disk representations for multiscale images and labels (ZarrArray), as well as points and shapes (DuckDB-backed tables). Includes handling of coordinate transformation systems and spatial utilities for cropping, masking, and querying. Integrates tabular annotations as 'SingleCellExperiment's (via 'anndataR'), enabling interoperable spatial omics workflows across R and Python.https://github.com/r-universe/biocstaging/actions/runs/26768238251Mon, 01 Jun 2026 12:18:51 GMTspatialdataR0.99.41successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/spatialdataRSpatialData.RmdSpatialData.htmlspatialdataR2023-04-27 14:17:422026-06-01 12:18:51marinif@uni-mainz.de (Federico Marini)KEGGemUP retrieves and renders interactively KEGG pathway graphs. The retrieval makes full use of the caching functionality to avoid unnecessary download processes. The interactivity of the graph is warranted via the visNetwork interface to the vis.js library, fully supporting bindings to be used in Shiny for further operations.https://github.com/r-universe/biocstaging/actions/runs/26507739927Wed, 27 May 2026 09:59:02 GMTKEGGemUP0.99.0successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/KEGGemUPKEGGemUP_userguide.RmdKEGGemUP_userguide.htmlThe KEGGemUP User's Guide2026-05-27 09:59:022026-05-27 09:59:02abassi.nejla96@gmail.com (Najla Abassi)EMMA is a package that provides a provenance-aware execution framework for functional enrichment analyses. It allows users to run enrichment analyses using existing tools and workflows while explicitly capturing analytical parameters during runtime, and returns the native enrichment results output together with structured metadata.https://github.com/r-universe/biocstaging/actions/runs/26162671077Wed, 20 May 2026 11:29:49 GMTEMMA0.99.3successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/EMMAIntroduction_to_EMMA.RmdIntroduction_to_EMMA.htmlThe EMMA User's Guide - Enrichment Method MAtters2022-09-11 10:08:042026-05-19 13:48:32marinif@uni-mainz.de (Federico Marini)This package provides a dedicated panel to assist the sample identification within a single iSEE web-application. The main functionality of this package can be adopted to efficiently select samples (e.g. cells) that need to be identified and annotated in the analysis workflow. With iSEEid, the iSEE framework fully qualifies to be an ideal companion for assigning appropriate labels to large omics datasets.https://github.com/r-universe/biocstaging/actions/runs/26112279736Tue, 19 May 2026 14:06:01 GMTiSEEid0.99.0successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/iSEEidIntroduction_to_iSEEid.RmdIntroduction_to_iSEEid.htmlIntroduction to iSEEid - Using iSEE to annotate single cells2024-09-02 15:35:172026-05-19 14:03:46stvjc@channing.harvard.edu (Vincent Carey)Provides a tidyverse-oriented user interface to Gene Ontology data via the Semantic SQL representation, accessed through DuckDB. Replaces the GO.db + AnnotationDbi::select nexus with lazy tibble-based operations for term lookup, ancestor/descendant traversal, and gene-GO annotation queries. The Semantic SQL resource is managed by the ontoProc2 package via BiocFileCache.https://github.com/r-universe/biocstaging/actions/runs/25881234685Thu, 14 May 2026 18:25:07 GMTGO.ddb0.99.4failurehttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/GO.ddbstvjc@channing.harvard.edu (Vince Carey)This is a parquet-based representation of GENCODE gene models v49 for Homo sapiens. Parquet is chosen to reduce footprint, to support tidyverse-oriented operations natively, and to provide opportunities for cloud-backed annotation services. Community contributions to functionality and architecture are welcome.https://github.com/r-universe/biocstaging/actions/runs/25864951316Thu, 14 May 2026 12:27:56 GMTTxParq.Hs.gencode.v490.99.2successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/TxParq.Hs.gencode.v49TxParq.Hs.gencode.v49.RmdTxParq.Hs.gencode.v49.htmlTxParq.Hs.gencode.v49: Parquet transformation of TxDb.Hs with Gencode v492026-05-12 12:59:532026-05-13 17:43:45stvjc@channing.harvard.edu (Vincent Carey)This package provides ontology facilities based on INCAtools Semantic SQL. Tooling is provided to retrieve and cache SQLite databases representing curated ontologies. ontologyIndex ontology_index instances can be produced. Anthropic's Claude was used in the development of S7 classes and methods and in the production of documentation.https://github.com/r-universe/biocstaging/actions/runs/25704579127Mon, 11 May 2026 23:01:49 GMTontoProc20.99.20successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/ontoProc2celltoprotein.Rmdcelltoprotein.htmlcelltoprotein -- connecting Cell and Protein Ontologies2026-03-25 10:00:262026-03-31 20:21:25ontoProc2.RmdontoProc2.htmlontoProc2 -- leveraging semantic SQL for ontology analysis in Bioconductor2025-10-27 12:07:102026-05-11 21:17:14uberonpeek.Rmduberonpeek.htmluberonpeek -- a look at UBERON ontology, etc., with ontoProc22023-09-07 20:03:532026-03-31 18:12:14hpages.on.github@gmail.com (Hervé Pagès)The package implements a set of S4 classes (DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment) for representing multiple sequence alignments.https://github.com/r-universe/biocstaging/actions/runs/25514382039Thu, 07 May 2026 17:14:12 GMTMultipleAlignment0.99.1successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/MultipleAlignmentMultipleAlignments.RmdMultipleAlignments.htmlMultipleAlignment Objects2026-04-30 00:33:162026-04-30 00:33:16lori.shepherd@roswellpark.org (Lori Shepherd)What the package does (one paragraph).https://github.com/r-universe/biocstaging/actions/runs/26396366522Wed, 29 Jun 2022 14:50:59 GMTspbtest30.99.119successhttps://biocstaging.r-universe.devhttps://github.com/Bioconductor/spbtest3test3.Rmdtest3.htmlBioc Tes32018-05-25 11:47:522018-05-25 13:31:48test2.Rmdtest2.htmlBiocFileCache: Managing File Resources Across Sessions2018-05-25 11:47:522018-06-14 12:28:32spbtest3.Rnwspbtest3.pdfspbtest32016-09-27 12:52:582018-05-25 11:47:52test.Rnwtest.pdftest2018-05-25 11:47:522018-05-25 13:31:48lori.shepherd@roswellpark.org (Lori Shepherd)What the package does? (one paragraph).https://github.com/r-universe/biocstaging/actions/runs/26354659479Mon, 24 Feb 2020 18:27:04 GMTspbtest50.99.1successhttps://biocstaging.r-universe.devhttps://github.com/Bioconductor/spbtest5spbtest5.Rnwspbtest5.pdfspbtest52020-02-24 18:09:482020-02-24 18:09:48