Research & Science · UMAP

Analyze single-cell data with core Scarf, the out-of-core Zarr DataStore library with immutable artifacts and pipeline runs.

NygenAnalytics/scarf

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or…

K-Dense-AI/scientific-agent-skills

BPX level command skill. An agent skill from wilddogjp/openbpx.

wilddogjp/openbpx

Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions)…

GPTomics/bioSkills

Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).

FreedomIntelligence/OpenClaw-Medical-Skills

Stage 2 of the spatial transcriptomics workflow — normalize 10x Visium data and cluster spatial spots.

QING1105/ezST

A skill your agent uses when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE…

aipoch/medical-research-skills

Dimensionality reduction and graph-based clustering for single-cell RNA-seq with Scanpy (Python) and Seurat (R).

GPTomics/bioSkills

Plots spatial transcriptomics expression, clusters, and annotations on tissue using Squidpy and Scanpy.

GPTomics/bioSkills

Integrates single-cell paired TCR/BCR (10x VDJ, AIRR, dandelion, BD Rhapsody) with gene expression in an AnnData/MuData object using scirpy - chain-pairing QC, clonotype definition, clonal…

GPTomics/bioSkills

Standard single-cell RNA-seq analysis pipeline. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference.

jaechang-hits/SciAgent-Skills

Harmony batch correction for scRNA-seq and other omics. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

A skill your agent uses whenever the user wants reproducible CS/AI experiments, model evaluation, regression/classification/clustering analyses, bioinformatics workflows, QC, differential…

Citrus-bit/Anaxa

Load when integrating multi-sample scRNA-seq with Harmony, scVI, scANVI, BBKNN, Scanorama, SIMBA, or supported R-backed methods to remove batch effects.

TianGzlab/OmicsClaw

Load when building the neighbour graph, embedding (UMAP/t-SNE/diffmap/PHATE), and clustering (Leiden/Louvain) on a normalised single-cell AnnData.

TianGzlab/OmicsClaw

Load when preprocessing a single-cell ATAC peak × cell AnnData via Signac-style TF-IDF + LSI + Leiden, producing a clustered UMAP-ready object.

TianGzlab/OmicsClaw