Waldron Lab at the CUNY SPH

Repositories

• cBioPortalData

  Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
  R 5 19 6 0 Updated Aug 23, 2020

• config

  A repository for common configuration scripts
  Vim script 0 0 0 0 Updated Aug 15, 2020

• HMP16SData

  16S rRNA Sequencing Data from the Human Microbiome Project

  bioconductor experimenthub hmp bioconductor-package
  R Artistic-2.0 3 9 1 0 Updated Aug 11, 2020

• HGNChelper

  Identify and correct invalid gene symbols
  R 6 14 1 0 Updated Aug 10, 2020

• testPkg
  R 14 0 1 0 Updated Aug 4, 2020

• MicrobiomeOntology
  Dockerfile 0 1 5 (1 issue needs help) 0 Updated Aug 4, 2020

• curatedMetagenomicDataCuration

  Curation for curatedMetagenomicData
  R 11 12 11 (3 issues need help) 0 Updated Aug 3, 2020

• AnVILWorkshop

  AnVIL/Terra workshop for BioC2020
  Dockerfile 3 1 0 0 Updated Jul 30, 2020

• CNVWorkshop

  Workshop for CNV analysis with Bioconductor
  R 0 13 1 0 Updated Jul 28, 2020

• MultiAssayWorkshop

  Material for the MultiAssayExperiment / curatedTCGAData workshop
  Dockerfile 1 5 0 0 Updated Jul 28, 2020

• enrichOmics

  Functional enrichment analysis of high-throughput omics data
  Dockerfile Artistic-2.0 7 15 2 0 Updated Jul 28, 2020

• PublicDataResources

  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…
  Dockerfile 4 10 2 0 Updated Jul 28, 2020

• SingleCellMultiModal

  Single Cell multimodal data scripts for downloading datasets
  R 4 7 3 1 Updated Jul 28, 2020

• MultiAssayExperiment

  Bioconductor package for management of multi-assay data

  r genomics tcga bioconductor nci-itcr bioconductor-package
  R 28 44 8 0 Updated Jul 21, 2020

• TCGAutils

  Toolbox package for organizing and working with TCGA data

  utilities tcga bioconductor-package
  R 6 6 0 0 Updated Jul 11, 2020

• CNVRanger

  Functionality for CNV analysis
  R 2 1 3 0 Updated Jul 10, 2020

• presentations

  A repository for public presentations
  HTML CC0-1.0 9 2 1 0 Updated Jul 7, 2020

• curatedmetagenomics
  Shell 4 1 14 (1 issue needs help) 0 Updated Jun 30, 2020

• GSEABenchmarkeR

  Reproducible GSEA Benchmarking

  bioconductor-package
  R Artistic-2.0 3 9 2 0 Updated Jun 23, 2020

• subtypeHeterogeneity

  Tumor subclonality of expression-based cancer subtypes
  R 0 2 0 0 Updated Jun 10, 2020

• curatedMetagenomicData

  Curated and processed metagenomic data through ExperimentHub

  bioconductor bioconductor-package
  R Artistic-2.0 20 64 23 (3 issues need help) 0 Updated Jun 9, 2020

• AnVILWorkshop-1

  Forked from shbrief/AnVILWorkshop

  AnVIL/Terra workshop for BioC2020
  Dockerfile 1 0 0 0 Updated Jun 9, 2020

• curatedMetagenomicDataSQL

  SQL database, API, and related functions for curatedMetagenomicData
  Python 1 1 1 0 Updated Jun 5, 2020

• data-science-seminar

  Topics In Data Science and Bioinformatics
  HTML 30 65 3 0 Updated Jun 3, 2020

• bioconductor

  Docker container built on bioconductor/bioconductor_docker
  Shell 3 8 2 (1 issue needs help) 0 Updated May 12, 2020

• schematics
  MIT 0 0 0 0 Updated May 11, 2020

• bioc_docker
  Shell 0 1 0 0 Updated May 8, 2020

• newsfeed

  Compile NEWS files from several packages
  R 0 0 0 0 Updated May 6, 2020

• bugSigSimple

  Simple exploratory analysis of curated microbe signatures
  R 2 0 0 0 Updated May 2, 2020

• pensim

  Tuning and nested cross-validation for L1, L2, and Elastic Net penalized regression
  R 0 0 0 0 Updated Apr 17, 2020