A list of repositories discovered on GitHub. The table is sortable by clicking on headers and searchable via the search box.
| Repository | Owner | Description | Stars | Last Updated |
|---|---|---|---|---|
| awesome-cancer-variant-resources | seandavi | A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants. | 315 | 2025-03-06 |
| MultiAssayExperiment | waldronlab | Bioconductor package for management of multi-assay data | 72 | 2025-05-06 |
| BiocParallel | Bioconductor | Bioconductor facilities for parallel evaluation | 68 | 2025-06-20 |
| SpatialExperiment | drighelli | 66 | 2025-05-28 | |
| HGNChelper | waldronlab | Identify and correct invalid gene symbols | 58 | 2024-11-16 |
| curatedTCGAData | waldronlab | Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects | 44 | 2025-05-05 |
| cBioPortalData | waldronlab | Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment | 33 | 2025-07-02 |
| TCGAutils | waldronlab | Toolbox package for organizing and working with TCGA data | 28 | 2025-07-14 |
| DelayedArray | Bioconductor | A unified framework for working transparently with on-disk and in-memory array-like datasets | 27 | 2025-07-11 |
| BiocPkgTools | seandavi | Computable build reports, package metadata, and download stats from the Bioconductor project | 21 | 2025-07-15 |
| MultiAssayWorkshop | waldronlab | Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment | 21 | 2025-07-02 |
| enrichOmics | waldronlab | Functional enrichment analysis of high-throughput omics data | 20 | 2025-01-06 |
| AnnotationHub | Bioconductor | Client for the Bioconductor AnnotationHub web resource | 19 | 2025-07-14 |
| SingleCellMultiModal | waldronlab | Single Cell multimodal data scripts for downloading datasets | 17 | 2025-06-12 |
| GenomicSuperSignature | shbrief | Interpretation of RNAseq experiments through robust, efficient comparison to public databases | 16 | 2025-05-16 |
| PublicDataResources | waldronlab | Public data resources and Bioconductor: The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources including the Gene Expression Omnibus GEO, Sequence Read Archive SRA, the Genomic Data Commons GDC, and Bioconductor-hosted curated data resources for metagenomics, pharmacogenomics PharmacoDB, and The Cancer Genome Atlas. | 14 | 2025-05-12 |
| GSEABenchmarkeR | waldronlab | Reproducible GSEA Benchmarking | 13 | 2025-05-08 |
| BiocFileCache | Bioconductor | Manage Files Across Sessions | 13 | 2025-07-15 |
| HDF5Array | Bioconductor | HDF5 datasets as array-like objects in R | 12 | 2025-05-28 |
| curatedOvarianData | waldronlab | The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer | 11 | 2025-05-05 |
| ExperimentHub | Bioconductor | Client to access ExperimentHub resources | 10 | 2025-07-14 |
| BiocOncoTK | vjcitn | Bioconductor components for general cancer genomics | 10 | 2023-02-05 |
| CNVRanger | waldronlab | Functionality for CNV analysis | 9 | 2025-05-08 |
| SparseArray | Bioconductor | High-performance sparse data representation and manipulation in R | 9 | 2025-06-18 |
| MultiAssayExperiment.TCGA | waldronlab | The pipeline to produce TCGA data as MultiAssayExperiment objects | 7 | 2023-05-16 |
| S4Arrays | Bioconductor | Foundation of array-like containers in Bioconductor | 6 | 2025-05-28 |
| RaggedExperiment | Bioconductor | Matrix-like representations of mutation and CN data | 5 | 2025-07-10 |
| scConform | ccb-hms | Uncertainty quantification for cell type annotation using conformal inference | 4 | 2024-07-25 |
| state-cancer-profile-scraper | seandavi | Bulk access and download state cancer profiles data | 3 | 2025-07-01 |
| OmicsMLRepoData | waldronlab | Translate Bioconductor resources into AI/ML-ready format + Manual curation/harmonization of the metadata for improved usability | 3 | 2025-07-10 |
| GenomicFiles | Bioconductor | Distributed computing by file or by range | 2 | 2025-05-28 |
| YESCDS | vjcitn | Cancer Data Science resources for DFCI YES for CURE | 2 | 2024-10-30 |
| OmicsMLRepoR | shbrief | Bioconductor package to access the harmonized metadata through ontology | 2 | 2025-06-07 |
| refinebioc | seandavi | The bridge between refine.bio and Bioconductor | 2 | 2025-03-05 |
| BiocBuildDB | seandavi | Longitudinal Bioc build database | 1 | 2025-03-20 |
| h5mread | Bioconductor | A fast HDF5 reader | 1 | 2025-05-28 |
| oncoKBData | waldronlab | Expose the Onco KB API via R / Bioconductor | 1 | 2025-05-09 |
| xenLite | vjcitn | Lightweight approach to managing Xenium experiments | 1 | 2024-11-27 |
| bedbaser | waldronlab | An R client for bedbase.org | 1 | 2025-07-15 |
| BiocHubsIngestR | Bioconductor | Helper package for users to upload data to temporary BiocHubsIngest endpoints | 1 | 2025-02-27 |
| curatedMetagenomicDataODM | shbrief | Genestack's Open Data Management (ODM) setup for curatedMetagenomicData curation | 1 | 2025-03-18 |
| TxRegInfra2 | vjcitn | Software for exploring transcriptional regulatory networks, currently using MongoDB documents for various genomic feature types | 1 | 2020-12-31 |
| TENxIO | waldronlab | Bioconductor interface to 10X files | 0 | 2025-05-08 |
| XeniumIO | waldronlab | software for importing 10X Xenium data | 0 | 2025-07-03 |
| hovernethelp | hpages | 0 | 2025-05-22 | |
| programets | nih-cfde | 0 | 2025-07-11 | |
| HGNCREST | waldronlab | Query the HGNC REST API with R | 0 | 2025-05-09 |
| VisiumIO | waldronlab | Import spaceranger output and 10X spatial data | 0 | 2025-05-07 |
| u24Project | bd4everyone | Tracking for project 1U24CA289073-01 | 0 | 2025-07-08 |