Repositories list

• BugSigDBExports

  Public
  BugSigDB data files

  R

  •3•1•5•0•Updated Jan 2, 2025Jan 2, 2025

• MicrobiomeBenchmarkDataAnalyses

  Public
  Analyses using the datasets provided by the MicrobiomeBenchmarkData package.

  HTML

  •

  Other

  •0•0•0•0•Updated Dec 31, 2024Dec 31, 2024

• VisiumIO

  Public
  Import spaceranger output and 10X spatial data

  rgenomicsbioconductor-package

  R

  •0•0•1•0•Updated Dec 30, 2024Dec 30, 2024

• cBioPortalData

  Public
  Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

  bioconductor-package

  R

  •13•31•4•0•Updated Dec 28, 2024Dec 28, 2024

• cMDClick

  Public
  R

  •0•0•1•1•Updated Dec 28, 2024Dec 28, 2024

• cMDMeta

  Public
  Dashboard for cMD

  curatedmetagenomicdata

  R

  •

  Other

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

• OmicsMLRepoData

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

  R

  •0•2•4•0•Updated Dec 26, 2024Dec 26, 2024

• MultiAssayExperiment

  Public
  Bioconductor package for management of multi-assay data

  genomicstcganci-itcr+ 3bioconductor-packagerbioconductor

  R

  •33•70•4•1•Updated Dec 23, 2024Dec 23, 2024

• BugSigDBEnrich

  Public
  A ShinyApp to perform enrichemnt analysis with BugSigDB signatures.

  HTML

  •0•0•4•0•Updated Dec 21, 2024Dec 21, 2024

• BugSigDB

  Public
  A microbial signatures database

  JavaScript

  •6•7•15•3•Updated Dec 18, 2024Dec 18, 2024

• TCGAutils

  Public
  Toolbox package for organizing and working with TCGA data

  utilitiesbioconductor-packagetcga

  R

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

• lefser

  Public
  R implementation of the LEfSe method

  bioconductor-package

  R

  •5•51•9•1•Updated Dec 16, 2024Dec 16, 2024

• XeniumIO

  Public
  software for importing 10X Xenium data

  R

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

• bugSigSimple

  Public
  Simple exploratory analysis of curated microbe signatures

  R

  •12•3•4•0•Updated Dec 6, 2024Dec 6, 2024

• TENxIO

  Public
  Bioconductor interface to 10X files

  bioconductor-package

  R

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

• bedbaser

  Public
  An R client for bedbase.org

  R

  •0•1•4•0•Updated Dec 4, 2024Dec 4, 2024

• bioconductor

  Public template
  Docker container built on bioconductor/bioconductor_docker

  Shell

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

• taxPPro

  Public
  R

  •2•1•1•1•Updated Nov 21, 2024Nov 21, 2024

• SingleCellMultiModal

  Public
  Single Cell multimodal data scripts for downloading datasets

  bioconductor-package

  R

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

• HGNChelper

  Public
  Identify and correct invalid gene symbols

  R

  •9•55•4•0•Updated Nov 16, 2024Nov 16, 2024

• HGNCREST

  Public
  Query the HGNC REST API with R

  R

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• curatedTCGAData

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

  bioconductor-package

  R

  •7•44•7•0•Updated Nov 13, 2024Nov 13, 2024

• bugphyzz

  Public
  Harmonized annotation of microbial physiology

  R

  •6•6•7•0•Updated Oct 30, 2024Oct 30, 2024

• bugsigdbr

  Public
  R-side access to published microbial signatures from BugSigDB

  bioconductor-package

  R

  •

  GNU General Public License v3.0

  •3•3•3•0•Updated Oct 30, 2024Oct 30, 2024

• terraTCGAdata

  Public
  TCGA data access on Terra

  bioconductor-package

  R

  •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• MicrobiomeBenchmarkData

  Public
  Data for benchmarking in microbiome research.

  bioconductor-package

  R

  •0•0•3•0•Updated Oct 30, 2024Oct 30, 2024

• GSEABase

  Public
  Gene set enrichment data structures and methods

  R

  •12•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• GSEABenchmarkeR

  Public
  Reproducible GSEA Benchmarking

  bioconductor-package

  R

  •

  Other

  •4•13•2•0•Updated Oct 30, 2024Oct 30, 2024

• curatedOvarianData

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

  bioconductor-package

  R

  •3•11•0•0•Updated Oct 30, 2024Oct 30, 2024

• CNVRanger

  Public
  Functionality for CNV analysis

  bioconductor-package

  R

  •6•7•13•0•Updated Oct 30, 2024Oct 30, 2024