Repositories list

• BugSigDBExports

  Public
  BugSigDB data files

  r01ca230551

  r01ca230551

  R

  •4•3•5•1•Updated Mar 7, 2026Mar 7, 2026

• czieoss6-biocgpu

  Public
  Website tracking repositories related to czieoss6-biocgpu

  0•0•0•0•Updated Mar 7, 2026Mar 7, 2026

• BugSigDB

  Public
  A microbial signatures database

  r01ca230551

  r01ca230551

  PHP

  •8•8•17•5•Updated Mar 6, 2026Mar 6, 2026

• curatedMetagenomicDataCuration

  Public
  Sample Metadata Curation for curatedMetagenomicData

  r01ca230551

  r01ca230551

  R

  •24•30•20•1•Updated Mar 5, 2026Mar 5, 2026

• bioanalyzer-backend

  Public
  Streamline BugSigDB curation with AI-powered scientific paper analysis. Automatically extracts essential microbiome study metadata from research papers, reducin…

  pythonapibioinformatics+ 5

  pythonapibioinformaticsaimlmicrobiomencbipaper-analysis

  Python

  •0•0•8•0•Updated Mar 5, 2026Mar 5, 2026

• newsfeed

  Public
  Compile NEWS files from several packages

  R

  •0•0•0•0•Updated Mar 4, 2026Mar 4, 2026

• curator-desk

  Public
  Curator dashboard for reviewing BioAnalyzer predictions — sortable table, field-level feedback, submit via GitHub Issues & PRs.

  R

  •0•0•2•0•Updated Mar 4, 2026Mar 4, 2026

• imageFeatureTCGA

  Public
  R

  •1•1•7•0•Updated Mar 3, 2026Mar 3, 2026

• imageTCGAutils

  Public
  Misc. scripts for handling cancerdatasci data

  R

  •1•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• bugSigSimple

  Public
  Simple exploratory analysis of curated microbe signatures

  r01ca230551

  r01ca230551

  R

  •16•4•2•1•Updated Mar 2, 2026Mar 2, 2026

• config

  Public
  A repository for common configuration scripts

  Shell

  •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• bugphyzzExports

  Public
  r01ca230551

  r01ca230551

  R

  •1•1•3•0•Updated Mar 1, 2026Mar 1, 2026

• bedbaser

  Public
  An R client for bedbase.org

  u24ca289073

  u24ca289073

  R

  •2•2•5•0•Updated Feb 27, 2026Feb 27, 2026

• HistoImagePlot

  Public
  R

  •1•0•0•0•Updated Feb 25, 2026Feb 25, 2026

• cBioPortalData

  Public
  Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

  nci-itcrbioconductor-packageu24ca289073

  nci-itcrbioconductor-packageu24ca289073

  R

  •13•34•6•0•Updated Feb 24, 2026Feb 24, 2026

• BugSigDBcuration

  Public
  For documenting issues related to BugSigDB curation.

  r01ca230551

  r01ca230551

  13•17•134•3•Updated Feb 17, 2026Feb 17, 2026

• OmicsMLRepoData

  Public
  Translate Bioconductor resources into AI/ML-ready format + Manual curation/harmonization of the metadata for improved usability

  u24ca289073

  u24ca289073

  R

  •0•4•9•2•Updated Feb 15, 2026Feb 15, 2026

• TENxIO

  Public
  Bioconductor interface to 10X files

  bioconductor-packageu24ca289073

  bioconductor-packageu24ca289073

  R

  •0•1•1•0•Updated Feb 12, 2026Feb 12, 2026

• curatedMetagenomicData

  Public
  Curated Metagenomic Data of the Human Microbiome

  bioconductorexperimenthubbioconductor-package+ 1

  bioconductorexperimenthubbioconductor-packager01ca230551

  R

  •

  Artistic License 2.0

  •31•151•17•1•Updated Jan 21, 2026Jan 21, 2026

• shinyhomepage

  Public
  Build the index.html for the SPH shiny website

  R

  •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

• bugsigdbr

  Public
  R-side access to published microbial signatures from BugSigDB

  bioconductor-packager01ca230551

  bioconductor-packager01ca230551

  R

  •

  GNU General Public License v3.0

  •3•5•7•0•Updated Dec 29, 2025Dec 29, 2025

• VisiumIO

  Public
  Import spaceranger output and 10X spatial data

  rgenomicsbioconductor-package+ 1

  rgenomicsbioconductor-packageu24ca289073

  R

  •2•2•0•0•Updated Dec 24, 2025Dec 24, 2025

• XeniumIO

  Public
  software for importing 10X Xenium data

  u24ca289073

  u24ca289073

  R

  •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

• TCGAutils

  Public
  Toolbox package for organizing and working with TCGA data

  utilitiestcgabioconductor-package+ 1

  utilitiestcgabioconductor-packageu24ca289073

  R

  •7•28•1•0•Updated Dec 11, 2025Dec 11, 2025

• cheatsheets

  Public
  WaldronLab Cheat Sheets

  MIT License

  •0•1•0•0•Updated Nov 18, 2025Nov 18, 2025

• lefser

  Public
  R implementation of the LEfSe method

  bioconductor-packager01ca230551

  bioconductor-packager01ca230551

  R

  •7•63•8•1•Updated Nov 17, 2025Nov 17, 2025

• curatedTCGAData

  Public
  Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

  bioconductor-packageu24ca289073

  bioconductor-packageu24ca289073

  R

  •9•44•8•0•Updated Nov 17, 2025Nov 17, 2025

• doppelgangR

  Public
  Identify possibly duplicate samples in a list of ExpressionSets

  bioconductor-package

  bioconductor-package

  R

  •4•5•0•0•Updated Nov 17, 2025Nov 17, 2025

• CNVRanger

  Public
  Functionality for CNV analysis

  bioconductor-packageu24ca289073

  bioconductor-packageu24ca289073

  R

  •7•8•14•0•Updated Nov 17, 2025Nov 17, 2025

• SingleCellMultiModal

  Public
  Single Cell multimodal data scripts for downloading datasets

  bioconductor-packageu24ca289073

  bioconductor-packageu24ca289073

  R

  •9•18•1•0•Updated Nov 17, 2025Nov 17, 2025