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 |
|---|---|---|---|---|
| curatedMetagenomicData | waldronlab | Curated Metagenomic Data of the Human Microbiome | 138 | 2025-06-04 |
| lefser | waldronlab | R implementation of the LEfSe method | 59 | 2025-04-22 |
| curatedMetagenomicDataAnalyses | waldronlab | Analyses in R and Python Using curatedMetagenomicData | 32 | 2025-04-01 |
| curatedMetagenomicDataCuration | waldronlab | Sample Metadata Curation for curatedMetagenomicData | 29 | 2025-07-16 |
| MicrobiomeWorkshop | waldronlab | A workshop on microbiome analysis using Bioconductor | 15 | 2019-06-20 |
| BugSigDBcuration | waldronlab | For documenting issues related to BugSigDB curation. | 14 | 2025-03-27 |
| HMP16SData | waldronlab | 16S rRNA Sequencing Data from the Human Microbiome Project | 9 | 2025-05-05 |
| curatedMetagenomicsNextflow | seandavi | Curated Metagenomics Data Nextflow workflows | 8 | 2025-07-03 |
| BugSigDB | waldronlab | A microbial signatures database | 8 | 2025-07-09 |
| bugsigdbr | waldronlab | R-side access to published microbial signatures from BugSigDB | 4 | 2025-05-29 |
| bugSigSimple | waldronlab | Simple exploratory analysis of curated microbe signatures | 4 | 2025-07-10 |
| curatedMetagenomicDataTerminal | waldronlab | A Command-Line Interface for curatedMetagenomicData | 3 | 2021-11-13 |
| lefserBenchmarking | shbrief | Benchmarking examples of lefser against LEfSe and microbiomeMarker | 3 | 2024-11-19 |
| BugSigDBExports | waldronlab | BugSigDB data files | 3 | 2025-07-17 |
| curatedMetagenomicDataPipeline | waldronlab | The Preprocessing Pipeline for curatedMetagenomicData | 2 | 2021-10-14 |
| MicrobiomeBenchmarkDataPrep | waldronlab | Preparation of datasets for MicrobiomeBenchmarkData | 1 | 2024-09-02 |
| curatedMetagenomicDataODM | shbrief | Genestack's Open Data Management (ODM) setup for curatedMetagenomicData curation | 1 | 2025-03-18 |
| BugSigDBStats | waldronlab | BugSigDB Stats and Analysis | 1 | 2025-06-30 |
| bugphyzzExports | waldronlab | 1 | 2025-07-13 | |
| MicrobiomeBenchmarkDataLefse | waldronlab | Running lefse with lefse-conda, lefser, and microbiomeMarker | 1 | 2024-09-25 |
| taxPPro | waldronlab | 1 | 2025-06-30 | |
| bugphyzzAnalyses | waldronlab | Analyses with data and signatures imported from the bugphyzz package. | 1 | 2024-06-28 |
| BugSigDBEnrich | waldronlab | A ShinyApp to perform enrichemnt analysis with BugSigDB signatures. | 0 | 2025-01-21 |
| taxPProValidation | waldronlab | Code for validation analyses for prediction of annotations in bugphyzz | 0 | 2024-07-05 |
| PublicMicrobiomeProject | waldronlab | Tracking for project R01ca230551: Exploiting Public Metagenomic Data to Uncover Cancer-Microbiome Relationships | 0 | 2025-07-06 |
| nextflow_telemetry | seandavi | Python web api for nextflow web callbacks | 0 | 2025-03-13 |
| MicrobiomeBenchmarkData | waldronlab | Data for benchmarking in microbiome research. | 0 | 2025-04-16 |
| cMDMeta | waldronlab | Dashboard for cMD | 0 | 2024-12-28 |
| MicrobiomeBenchmarkDataAnalyses | waldronlab | Analyses using the datasets provided by the MicrobiomeBenchmarkData package. | 0 | 2025-04-18 |
| BugSigDBPaper | waldronlab | Figures and Tables for the BugSigDB paper | 0 | 2023-10-19 |
| ncbitaxon | waldronlab | Hosting the NCBI taxnomy | 0 | 2024-08-21 |
| curatedMetagenomicDataShinyApp | waldronlab | ShinyApp for curatedMetagenomicDataCuraiton | 0 | 2021-11-29 |