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hossainlab

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   Omics Dataset Retrieval · hossainlab bundle

   Systematically retrieve, deduplicate, classify, and relevance-audit publicly available omics datasets for a user-specified disease, phenotype, gene, or biological process. Covers all major omics types (transcriptomics, proteomics, metabolomics, epigenomics, genomics, single-cell, spatial, lipidomics, multi-omics) across the broadest set of public repositories (GEO, SRA, ArrayExpress, PRIDE, OmicsDI, CELLxGENE, GDC/TCGA, ENCODE, and 20+ more). Use when the user asks to find, survey, catalog, or map available omics/sequencing datasets for a topic. Does NOT download raw data or run downstream analysis.
   0 installs
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   Bulk Rnaseq Counts To De Deseq2 · hossainlab bundle

   Run differential expression analysis on bulk RNA-seq count data with DESeq2 (R). Covers DESeqDataSet construction from a count matrix, tximport (Salmon/Kallisto), featureCounts, or SummarizedExperiment; pre-filtering; design formulas (simple, batch, paired, interaction, multi-factor, LRT); result extraction by coefficient or contrast; log-fold-change shrinkage (apeglm/ashr); VST/rlog transformations; and exporting significant genes. Use when the user has RNA-seq counts and wants differential expression, DE genes, volcano/MA inputs, or a DESeq2 workflow.
   0 installs