Waldron Lab at the CUNY SPH
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BugSigDBExports
Publicczieoss6-biocgpu
PublicBugSigDB
Publicai-agent-skills
PublicA collection of AI agent skills relevant to our work, including analysis and development of R/Bioconductor packages + statistical and bioinformatic analysis.HistoImagePlot
PublicbugSigSimple
PublicSimple exploratory analysis of curated microbe signaturesbioanalyzer-backend
PublicStreamline BugSigDB curation with AI-powered scientific paper analysis. Automatically extracts essential microbiome study metadata from research papers, reducin…- Sample Metadata Curation for curatedMetagenomicData
curatedCRCData
PublicThe curatedCRCData package provides ExpressionSet data with curated metadata and microarray gene expression data from colorectal cancer tumors.imageTCGAutils
PublicTENxIO
PublicBioconductor interface to 10X filesbugphyzz
PublicHarmonized annotation of microbial physiologylefser
PublicR implementation of the LEfSe methodcuratedMetagenomicData
PublicCurated Metagenomic Data of the Human MicrobiomecBioPortalData
PublicIntegrate the cancer genomics portal, cBioPortal, using MultiAssayExperimentCNVRanger
PublicFunctionality for CNV analysisXeniumIO
Publicsoftware for importing 10X Xenium dataVisiumIO
PublicImport spaceranger output and 10X spatial dataimageFeatureTCGA
Publicbedbaser
PublicHMP16SData
Public16S rRNA Sequencing Data from the Human Microbiome ProjectcuratedOvarianData
PublicThe curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancerterraTCGAdata
PublicTCGA data access on TerraMicrobiomeBenchmarkData
PublicData for benchmarking in microbiome research.SingleCellMultiModal
PublicSingle Cell multimodal data scripts for downloading datasetsGSEABenchmarkeR
PublicReproducible GSEA Benchmarkingbugsigdbr
PublicR-side access to published microbial signatures from BugSigDBcuratedTCGAData
PublicCurated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment ObjectsMultiAssayExperiment
PublicBioconductor package for management of multi-assay datadoppelgangR
PublicIdentify possibly duplicate samples in a list of ExpressionSets
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