GitHub
python-math
Small Python utilities for math and text files.
☆ 858View skill
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GitHub
file-tools
Simple shell utilities for files and archives.
☆ 858View skill
GitHub
user-file-ops
Simple operations on user-provided text files including summarization.
☆ 858View skill
GitHub
frontend-design
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, artifacts, posters, or applications. Generates creative, poli...
☆ 851View skill
GitHub
flowmvi
FlowMVI usage guidance. Use when working with FlowMVI stores/containers, plugin pipelines, composing stores, decorators, or authoring plugins.
☆ 845View skill
GitHub
bulk-rna-seq-deconvolution-with-bulk2single
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-se...
☆ 834View skill
GitHub
data-stats-analysis
Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
☆ 834View skill
GitHub
string-protein-interaction-analysis-with-omicverse
Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
☆ 834View skill
GitHub
spatial-transcriptomics-tutorials-with-omicverse
Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.
☆ 834View skill
GitHub
omicverse-visualization-for-bulk-color-systems-and-single-cell-d
Guide users through OmicVerse plotting utilities showcased in the bulk, color system, and single-cell visualization tutorials, including venn/volcano charts, palette selection, and advanced embedding layouts.
☆ 834View skill
GitHub
bulk-rna-seq-differential-expression-with-omicverse
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. Use when a user has bulk count matrices a...
☆ 834View skill
GitHub
single2spatial-spatial-mapping
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
☆ 834View skill
GitHub
gsea-enrichment-analysis
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
☆ 834View skill
GitHub
data-export-excel
Export analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
☆ 834View skill
GitHub
data-export-pdf
Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
☆ 834View skill
GitHub
bulktrajblend-trajectory-interpolation
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
☆ 834View skill
GitHub
bulk-rna-seq-deseq2-analysis-with-omicverse
Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.
☆ 834View skill
GitHub
bulk-rna-seq-batch-correction-with-combat
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
☆ 834View skill
GitHub
single-trajectory-analysis
Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.
☆ 834View skill
GitHub
tcga-bulk-data-preprocessing-with-omicverse
Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.
☆ 834View skill
GitHub
single-cell-multi-omics-integration
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
☆ 834View skill
GitHub
single-cell-preprocessing-with-omicverse
Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.
☆ 834View skill
GitHub
data-transform
Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
☆ 834View skill
GitHub
single-cell-cellphonedb-communication-mapping
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
☆ 834View skill
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