Browse Skills

file-tools.md

787

1 export file-tools

2 from "trpc-group/trpc-agent-go"

3 Simple shell utilities for files and archives.

2026-01-06

user-file-ops.md

787

1 export user-file-ops

2 from "trpc-group/trpc-agent-go"

3 Simple operations on user-provided text files including summarization.

2026-01-06

bulk-rna-seq-deconvolution-with-bulk2single.md

783

1 export bulk-rna-seq-deconvolution-with-bulk2single

2 from "Starlitnightly/omicverse"

3 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-seq.

2026-01-04

single-cell-downstream-analysis.md

783

1 export single-cell-downstream-analysis

2 from "Starlitnightly/omicverse"

3 Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.

2026-01-04

bulk-wgcna-analysis-with-omicverse.md

783

1 export bulk-wgcna-analysis-with-omicverse

2 from "Starlitnightly/omicverse"

3 Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes.

2026-01-04

spatial-transcriptomics-tutorials-with-omicverse.md

783

1 export spatial-transcriptomics-tutorials-with-omicverse

2 from "Starlitnightly/omicverse"

3 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.

2026-01-04

single-cell-preprocessing-with-omicverse.md

783

1 export single-cell-preprocessing-with-omicverse

2 from "Starlitnightly/omicverse"

3 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.

2026-01-04

bulktrajblend-trajectory-interpolation.md

783

1 export bulktrajblend-trajectory-interpolation

2 from "Starlitnightly/omicverse"

3 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.

2026-01-04

single-cell-annotation-skills-with-omicverse.md

783

1 export single-cell-annotation-skills-with-omicverse

2 from "Starlitnightly/omicverse"

3 Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.

2026-01-04

single2spatial-spatial-mapping.md

783

1 export single2spatial-spatial-mapping

2 from "Starlitnightly/omicverse"

3 Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.

2026-01-04

single-cell-multi-omics-integration.md

783

1 export single-cell-multi-omics-integration

2 from "Starlitnightly/omicverse"

3 Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.

2026-01-04

single-cell-cellphonedb-communication-mapping.md

783

1 export single-cell-cellphonedb-communication-mapping

2 from "Starlitnightly/omicverse"

3 Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.

2026-01-04

data-viz-plots.md

783

1 export data-viz-plots

2 from "Starlitnightly/omicverse"

3 Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

2026-01-04

string-protein-interaction-analysis-with-omicverse.md

783

1 export string-protein-interaction-analysis-with-omicverse

2 from "Starlitnightly/omicverse"

3 Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.

2026-01-04

executive-briefing.md

783

1 export executive-briefing

2 from "anthropics/claude-agent-sdk-demos"

3 Transforms research findings into executive-ready briefings. Automatically activated when user mentions 'executive', 'briefing', 'C-suite', 'board', 'leadership', or 'presentation'.

2026-01-06

listener-creator.md

783

1 export listener-creator

2 from "anthropics/claude-agent-sdk-demos"

3 Creates event-driven email listeners that monitor for specific conditions (like urgent emails from boss, newsletters to archive, package tracking) and execute custom actions. Use when user wants to be notified about emails, automatically handle certain emails, or set up email automation workflows.

2026-01-06

single-trajectory-analysis.md

783

1 export single-trajectory-analysis

2 from "Starlitnightly/omicverse"

3 Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.

2026-01-04

bulk-rna-seq-deseq2-analysis-with-omicverse.md

783

1 export bulk-rna-seq-deseq2-analysis-with-omicverse

2 from "Starlitnightly/omicverse"

3 Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.

2026-01-04

single-cell-clustering-and-batch-correction-with-omicverse.md

783

1 export single-cell-clustering-and-batch-correction-with-omicverse

2 from "Starlitnightly/omicverse"

3 Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.

2026-01-04

data-transform.md

783

1 export data-transform

2 from "Starlitnightly/omicverse"

3 Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

2026-01-04

data-export-pdf.md

783

1 export data-export-pdf

2 from "Starlitnightly/omicverse"

3 Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

2026-01-04

data-stats-analysis.md

783

1 export data-stats-analysis

2 from "Starlitnightly/omicverse"

3 Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

2026-01-04

omicverse-visualization-for-bulk-color-systems-and-single-cell-d.md

783

1 export omicverse-visualization-for-bulk-color-systems-and-single-cell-d

2 from "Starlitnightly/omicverse"

3 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.

2026-01-04

bulk-rna-seq-batch-correction-with-combat.md

783

1 export bulk-rna-seq-batch-correction-with-combat

2 from "Starlitnightly/omicverse"

3 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.

2026-01-04