Data & Analytics · AnnData · For data scientists

Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.

davila7/claude-code-templates

Differential gene expression analysis for bulk RNA-seq count matrices using a DESeq2-like workflow in Python; use when you need Wald tests, FDR correction, and optional LFC shrinkage for…

aipoch/medical-research-skills

Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.

FreedomIntelligence/OpenClaw-Medical-Skills

Load when inferring TF → target gene regulatory networks on a normalised scRNA AnnData via pySCENIC (GRNBoost2 + cisTarget + AUCell) or correlation-based GRN fallback (when arboreto is unavailable…

TianGzlab/OmicsClaw

Load when inferring copy-number variation per spot on a preprocessed spatial AnnData with chromosome-annotated genes via infercnvpy (default — log-ratio sliding-window) or Numbat (R, allele-aware…

TianGzlab/OmicsClaw

Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS.

TianGzlab/OmicsClaw

Load when running spatial autocorrelation / hotspot / co-occurrence / neighbourhood-enrichment / Ripley K stats on a clustered spatial AnnData via squidpy.

TianGzlab/OmicsClaw