Repositories list

• OmicsMLRepoData

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

  u24ca289073

  R

  •0•2•4•0•Updated Jan 29, 2025Jan 29, 2025

• BugSigDBExports

  Public
  BugSigDB data files

  R

  •3•1•5•0•Updated Jan 29, 2025Jan 29, 2025

• MultiAssayExperiment

  Public
  Bioconductor package for management of multi-assay data

  rgenomicstcga+ 4bioconductornci-itcrbioconductor-packageu24ca289073

  R

  •34•70•2•2•Updated Jan 28, 2025Jan 28, 2025

• bedbaser

  Public
  An R client for bedbase.org

  u24ca289073

  R

  •0•1•4•0•Updated Jan 28, 2025Jan 28, 2025

• VisiumIO

  Public
  Import spaceranger output and 10X spatial data

  rgenomicsbioconductor-package+ 1u24ca289073

  R

  •0•0•2•0•Updated Jan 28, 2025Jan 28, 2025

• curatedMetagenomicData

  Public
  Curated Metagenomic Data of the Human Microbiome

  bioconductor-packagebioconductorexperimenthub

  R

  •

  Artistic License 2.0

  •31•130•13•1•Updated Jan 27, 2025Jan 27, 2025

• config

  Public
  A repository for common configuration scripts

  Shell

  •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

• bugSigSimple

  Public
  Simple exploratory analysis of curated microbe signatures

  R

  •13•3•4•0•Updated Jan 24, 2025Jan 24, 2025

• lefser

  Public
  R implementation of the LEfSe method

  bioconductor-package

  R

  •5•53•8•1•Updated Jan 23, 2025Jan 23, 2025

• BugSigDBEnrich

  Public
  A ShinyApp to perform enrichemnt analysis with BugSigDB signatures.

  HTML

  •0•0•4•0•Updated Jan 21, 2025Jan 21, 2025

• MicrobiomeBenchmarkDataAnalyses

  Public
  Analyses using the datasets provided by the MicrobiomeBenchmarkData package.

  R

  •

  Other

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• cBioPortalData

  Public
  Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

  nci-itcrbioconductor-packageu24ca289073

  R

  •13•33•6•0•Updated Jan 14, 2025Jan 14, 2025

• cMDClick

  Public
  R

  •0•0•1•0•Updated Jan 14, 2025Jan 14, 2025

• subtypeHeterogeneity

  Public
  Tumor subclonality of expression-based cancer subtypes

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

  R

  •0•6•1•0•Updated Jan 7, 2025Jan 7, 2025

• curatedMetagenomicDataAnalyses

  Public
  Analyses in R and Python Using curatedMetagenomicData

  bioconductormicrobiome-analysismicrobiome-data+ 1r

  Python

  •

  Creative Commons Attribution 4.0 International

  •9•29•5•1•Updated Jan 6, 2025Jan 6, 2025

• RaggedExperiment_SoftNote

  Public
  exploration of RaggedExperiment

  u24ca289073

  R

  •

  Creative Commons Zero v1.0 Universal

  •1•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• CNVWorkshop

  Public
  Workshop for CNV analysis with Bioconductor

  R

  •2•17•1•0•Updated Jan 6, 2025Jan 6, 2025

• doppelgangR

  Public
  Identify possibly duplicate samples in a list of ExpressionSets

  bioconductor-package

  R

  •3•5•1•0•Updated Jan 6, 2025Jan 6, 2025

• PublicDataResources

  Public
  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, pharmacoge…

  u24ca289073

  TeX

  •4•14•2•0•Updated Jan 6, 2025Jan 6, 2025

• curatedOvarianData

  Public
  The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer

  bioconductor-packageu24ca289073

  R

  •3•11•0•0•Updated Jan 6, 2025Jan 6, 2025

• enrichOmics

  Public
  Functional enrichment analysis of high-throughput omics data

  u24ca289073

  Dockerfile

  •

  Artistic License 2.0

  •11•20•2•0•Updated Jan 6, 2025Jan 6, 2025

• AnVILWorkshop

  Public
  AnVIL/Terra workshop for Bioconductor conference

  Dockerfile

  •

  Other

  •6•3•0•0•Updated Jan 6, 2025Jan 6, 2025

• taxPPro

  Public
  R

  •2•1•1•1•Updated Jan 6, 2025Jan 6, 2025

• BugSigDB

  Public
  A microbial signatures database

  JavaScript

  •7•7•16•0•Updated Jan 2, 2025Jan 2, 2025

• cMDMeta

  Public
  Dashboard for cMD

  curatedmetagenomicdata

  R

  •

  Other

  •0•0•0•0•Updated Dec 28, 2024Dec 28, 2024

• TCGAutils

  Public
  Toolbox package for organizing and working with TCGA data

  utilitiestcgabioconductor-package+ 1u24ca289073

  R

  •6•24•1•0•Updated Dec 16, 2024Dec 16, 2024

• XeniumIO

  Public
  software for importing 10X Xenium data

  u24ca289073

  R

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• TENxIO

  Public
  Bioconductor interface to 10X files

  bioconductor-packageu24ca289073

  R

  •0•0•1•0•Updated Dec 5, 2024Dec 5, 2024

• bioconductor

  Public template
  Docker container built on bioconductor/bioconductor_docker

  Shell

  •5•9•3•0•Updated Nov 22, 2024Nov 22, 2024

• SingleCellMultiModal

  Public
  Single Cell multimodal data scripts for downloading datasets

  bioconductor-packageu24ca289073

  R

  •9•17•1•0•Updated Nov 20, 2024Nov 20, 2024