Repositories list

• bioanalyzer-backend

  Public
  Streamline BugSigDB curation with AI-powered scientific paper analysis. Automatically extracts essential microbiome study metadata from research papers, reducing manual curation time and improving data quality for the BugSigDB database.

  pythonapibioinformatics+ 5aimlmicrobiomencbipaper-analysis

  Python

  •0•0•1•0•Updated Oct 30, 2025Oct 30, 2025

• czieoss6-biocgpu

  Public
  Website tracking repositories related to czieoss6-biocgpu

  0•0•0•0•Updated Oct 30, 2025Oct 30, 2025

• BugSigDB

  Public
  A microbial signatures database

  r01ca230551

  PHP

  •7•8•19•5•Updated Oct 29, 2025Oct 29, 2025

• bedbaser

  Public
  An R client for bedbase.org

  u24ca289073

  R

  •1•1•4•0•Updated Oct 27, 2025Oct 27, 2025

• OmicsMLRepoData

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

  u24ca289073

  R

  •0•3•5•0•Updated Oct 27, 2025Oct 27, 2025

• VisiumIO

  Public
  Import spaceranger output and 10X spatial data

  rgenomicsbioconductor-package+ 1u24ca289073

  R

  •2•1•3•0•Updated Oct 24, 2025Oct 24, 2025

• lefser

  Public
  R implementation of the LEfSe method

  bioconductor-packager01ca230551

  R

  •6•59•10•1•Updated Oct 24, 2025Oct 24, 2025

• doppelgangR

  Public
  Identify possibly duplicate samples in a list of ExpressionSets

  bioconductor-package

  R

  •4•5•0•0•Updated Oct 24, 2025Oct 24, 2025

• curatedTCGAData

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

  bioconductor-packageu24ca289073

  R

  •9•43•8•0•Updated Oct 24, 2025Oct 24, 2025

• SingleCellMultiModal

  Public
  Single Cell multimodal data scripts for downloading datasets

  bioconductor-packageu24ca289073

  R

  •9•17•1•0•Updated Oct 24, 2025Oct 24, 2025

• shinyhomepage

  Public
  Build the index.html for the SPH shiny website

  R

  •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

• BioAnalyzer

  Public
  LLM for identifying Curatable Papers from PUMBED

  Python

  •1•0•2•0•Updated Oct 20, 2025Oct 20, 2025

• BugSigDBExports

  Public
  BugSigDB data files

  r01ca230551

  R

  •4•3•4•0•Updated Oct 12, 2025Oct 12, 2025

• curatedMetagenomicDataAnalyses

  Public
  Analyses in R and Python Using curatedMetagenomicData

  rbioconductormicrobiome-analysis+ 2microbiome-datar01ca230551

  Python

  •

  Creative Commons Attribution 4.0 International

  •8•32•4•0•Updated Oct 9, 2025Oct 9, 2025

• TENxIO

  Public
  Bioconductor interface to 10X files

  bioconductor-packageu24ca289073

  R

  •0•0•1•0•Updated Oct 7, 2025Oct 7, 2025

• bugphyzzExports

  Public
  r01ca230551

  R

  •1•1•3•0•Updated Oct 5, 2025Oct 5, 2025

• curatedMetagenomicData

  Public
  Curated Metagenomic Data of the Human Microbiome

  bioconductorexperimenthubbioconductor-package+ 1r01ca230551

  R

  •

  Artistic License 2.0

  •32•143•16•1•Updated Sep 26, 2025Sep 26, 2025

• curatedMetagenomicDataCuration

  Public
  Sample Metadata Curation for curatedMetagenomicData

  r01ca230551

  R

  •24•29•28•1•Updated Sep 24, 2025Sep 24, 2025

• MultiAssayExperiment

  Public
  Bioconductor package for management of multi-assay data

  rgenomicstcga+ 4bioconductornci-itcrbioconductor-packageu24ca289073

  R

  •34•71•1•0•Updated Aug 18, 2025Aug 18, 2025

• ITCR-bioconductor

  Public
  Tracking for project 1U24CA289073-01

  u24ca289073

  HTML

  •

  MIT License

  •1•0•0•0•Updated Aug 14, 2025Aug 14, 2025

• PublicMicrobiomeProject

  Public
  Tracking for project R01ca230551: Exploiting Public Metagenomic Data to Uncover Cancer-Microbiome Relationships

  r01ca230551

  HTML

  •

  MIT License

  •1•0•1•0•Updated Aug 14, 2025Aug 14, 2025

• bugSigSimple

  Public
  Simple exploratory analysis of curated microbe signatures

  r01ca230551

  R

  •15•4•6•1•Updated Aug 11, 2025Aug 11, 2025

• BugSigDBStats

  Public
  BugSigDB Stats and Analysis

  r01ca230551

  HTML

  •5•2•5•0•Updated Aug 6, 2025Aug 6, 2025

• cBioPortalData

  Public
  Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

  nci-itcrbioconductor-packageu24ca289073

  R

  •13•33•7•0•Updated Jul 21, 2025Jul 21, 2025

• AppStatBio

  Public
  Applied Statistics for High-Throughput Biology

  MIT License

  •17•16•0•0•Updated Jul 18, 2025Jul 18, 2025

• TCGAutils

  Public
  Toolbox package for organizing and working with TCGA data

  utilitiestcgabioconductor-package+ 1u24ca289073

  R

  •7•28•1•0•Updated Jul 14, 2025Jul 14, 2025

• XeniumIO

  Public
  software for importing 10X Xenium data

  u24ca289073

  R

  •0•0•0•0•Updated Jul 3, 2025Jul 3, 2025

• MultiAssayWorkshop

  Public
  Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment

  bioconductortcga-datamultiassayexperiment+ 2multi-omic-datau24ca289073

  TeX

  •4•24•0•0•Updated Jul 2, 2025Jul 2, 2025

• subtypeHeterogeneity

  Public
  Tumor subclonality of expression-based cancer subtypes

  bioconductorcopy-number-variationovarian-cancer+ 3single-cell-rna-seqgistic2purecn

  R

  •0•6•0•0•Updated Jun 30, 2025Jun 30, 2025

• taxPPro

  Public
  r01ca230551

  R

  •2•1•1•1•Updated Jun 30, 2025Jun 30, 2025