Waldron Lab at the CUNY SPH

Repositories

• curatedMetagenomicDataHighLoad
  Shell 3 0 12 (1 issue needs help) 0 Updated May 26, 2020

• CNVRanger

  Functionality for CNV analysis
  R 1 1 2 0 Updated May 22, 2020

• curatedMetagenomicDataSQL

  SQL database, API, and related functions for curatedMetagenomicData
  Python 0 1 0 0 Updated May 20, 2020

• data-science-seminar

  Topics In Data Science and Bioinformatics
  HTML 30 42 3 0 Updated May 20, 2020

• MultiAssayExperiment

  Bioconductor package for management of multi-assay data

  r genomics tcga bioconductor nci-itcr bioconductor-package
  R 29 43 6 0 Updated May 14, 2020

• curatedMetagenomicDataCuration

  Curation for curatedMetagenomicData
  R 11 10 11 (3 issues need help) 0 Updated May 13, 2020

• bioconductor

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

• cBioPortalData

  Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
  R 3 15 4 0 Updated May 12, 2020

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

• curatedMetagenomicData

  Curated and processed metagenomic data through ExperimentHub

  bioconductor bioconductor-package
  R Artistic-2.0 19 59 24 (3 issues need help) 0 Updated May 8, 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 1 0 0 0 Updated May 2, 2020

• SingleCellMultiModal

  Single Cell multimodal data scripts for downloading datasets
  R 1 3 1 0 Updated May 1, 2020

• config

  A repository for common configuration scripts
  Vim script 0 0 0 0 Updated Apr 28, 2020

• HGNChelper

  Identify and correct invalid gene symbols
  R 6 10 2 (1 issue needs help) 0 Updated Apr 28, 2020

• subtypeHeterogeneity

  Tumor subclonality of expression-based cancer subtypes
  R 0 2 0 0 Updated Apr 26, 2020

• MultiAssayWorkshop

  Material for the MultiAssayExperiment / curatedTCGAData workshop
  R MIT 0 1 0 0 Updated Apr 17, 2020

• pensim

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

• curatedTCGAData

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

  bioconductor-package
  R 7 29 12 0 Updated Apr 13, 2020

• TCGAutils

  Toolbox package for organizing and working with TCGA data

  utilities tcga bioconductor-package
  R 6 6 0 0 Updated Apr 13, 2020

• GSEABenchmarkeR

  Reproducible GSEA Benchmarking

  bioconductor-package
  R Artistic-2.0 2 8 3 0 Updated Apr 12, 2020

• ProjectAsPackage

  Demonstration of the use of an R package to organize a data analysis project
  R 2 17 0 0 Updated Mar 30, 2020

• doppelgangR

  Identify possibly duplicate samples in a list of ExpressionSets
  R 4 3 2 0 Updated Mar 19, 2020

• HMP16SData

  16S rRNA Sequencing Data from the Human Microbiome Project

  bioconductor experimenthub hmp bioconductor-package
  R Artistic-2.0 3 8 0 0 Updated Mar 11, 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…
  TeX 3 3 0 1 Updated Mar 3, 2020

• presentations

  A repository for public presentations
  TeX CC0-1.0 8 2 1 0 Updated Mar 2, 2020

• AnVILWorkshop
  1 0 0 0 Updated Mar 2, 2020

• sratool
  Dockerfile MIT 0 0 0 0 Updated Feb 14, 2020

• awesome-bioinformatics-benchmarks

  Forked from j-andrews7/awesome-bioinformatics-benchmarks

  A curated list of bioinformatics bench-marking papers and resources.
  GPL-3.0 14 1 0 0 Updated Feb 10, 2020