Waldron Lab at the CUNY SPH

All

106 repositories

BugSigDBExports
Public
BugSigDB data files
R
•3•1•5•0•Updated Dec 14, 2024Dec 14, 2024
BugSigDB
Public
A microbial signatures database
JavaScript
•6•7•15•2•Updated Dec 12, 2024Dec 12, 2024
MicrobiomeBenchmarkDataAnalyses
Public
Analyses using the datasets provided by the MicrobiomeBenchmarkData package.
HTML
•
Other
•0•0•0•0•Updated Dec 12, 2024Dec 12, 2024
TCGAutils
Public
Toolbox package for organizing and working with TCGA data
utilities bioconductor-package tcga
R
•6•23•1•0•Updated Dec 11, 2024Dec 11, 2024
cmdMeta
Public
Dashboard for cMD
curatedmetagenomicdata
R
•
Other
•0•0•0•0•Updated Dec 11, 2024Dec 11, 2024
cBioPortalData
Public
Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
bioconductor-package
R
•13•31•4•0•Updated Dec 10, 2024Dec 10, 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
VisiumIO
Public
Import spaceranger output and 10X spatial data
r genomics bioconductor-package
R
•0•0•1•0•Updated Dec 5, 2024Dec 5, 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
BugSigDBEnrich
Public
A ShinyApp to perform enrichemnt analysis with BugSigDB signatures.
HTML
•0•0•4•0•Updated Nov 27, 2024Nov 27, 2024
bioconductor
Public template
Docker container built on bioconductor/bioconductor_docker
Shell
•5•8•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
MultiAssayExperiment
Public
Bioconductor package for management of multi-assay data
genomics tcga nci-itcr bioconductor-package r bioconductor
R
•32•70•4•0•Updated Nov 19, 2024Nov 19, 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
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 Nov 12, 2024Nov 12, 2024
lefser
Public
R implementation of the LEfSe method
bioconductor-package
R
•5•50•9•1•Updated Nov 4, 2024Nov 4, 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
HMP16SData
Public
16S rRNA Sequencing Data from the Human Microbiome Project
bioconductor bioconductor-package experimenthub hmp
R
•
Other
•5•9•0•0•Updated Oct 30, 2024Oct 30, 2024