Skill OpenCode
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not rated 113
+1 2mo ago A 6 tokens
113Stars on the repository
199Mods indexed here, across every type
2mo agoLast push, which is what freshness is scored on
noneNo LICENSE: all rights reserved, so bodies are not copied
pantheon-omics
146Skill OpenCode
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not rated 113
+1 2mo ago A 6 tokens
pantheon-openst
147Skill OpenCode
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not rated 113
+1 2mo ago A 6 tokens
Skill OpenCode
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not rated 113
+1 2mo ago A 9 tokens
pantheon-scfm
149Skill OpenCode
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not rated 113
+1 2mo ago A 7 tokens
pantheon-spatial
150Skill OpenCode
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not rated 113
+1 2mo ago A 6 tokens
Skill OpenCode
Query the KEGG REST API for biological pathways, pathway gene lists, and gene info. Use when users ask about metabolic/signaling pathways, pathway genes, KEGG IDs, or gene-to-pathway mapping.
not rated 113
+1 2mo ago A 48 tokens
Skill OpenCode
Define tumor scRNA-seq pipeline family and phase-1 demo target.
not rated 113
+1 2mo ago A 24 tokens
Skill OpenCode
Generate PLAN.yaml for detailed metagenomic analysis using R phyloseq-based functions.
not rated 113
+1 2mo ago A 22 tokens
Skill OpenCode
Generate PLAN.yaml for tumor scRNA-seq heterogeneity and trajectory analysis.
not rated 113
+1 2mo ago A 27 tokens
Skill OpenCode
Ligand-aware protein sequence design with LigandMPNN for small molecules, metals, cofactors, and DNA/RNA binding sites.
not rated 113
+1 2mo ago A 35 tokens
Skill OpenCode
Validate protein designs using AlphaFold2 structure prediction: select backend, run prediction, extract confidence metrics (pLDDT, pTM, ipTM, PAE), assess quality against thresholds, and troubleshoot runtime errors.
not rated 113
+1 2mo ago A 51 tokens
Skill OpenCode
Install and run RefHiC for reference-panel-guided Hi-C loop calling and TAD boundary annotation, including reference panel configuration, prediction, FDR-based selection, and output interpretation.
not rated 113
+1 2mo ago A 47 tokens
registry
158Skill OpenCode
Route user requests to domain, discipline, and candidate tumor scRNA-seq pipelines via SQLite pipeline routes.
not rated 113
+1 2mo ago A 23 tokens
Skill OpenCode
Generate structured tumor scRNA-seq analysis report.
not rated 113
+1 2mo ago A 19 tokens
Skill OpenCode
Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (obsp/varp), uns. Use for .h5ad/.zarr I/O, concatenation, scverse integration. For analysis use scanpy; for probabilistic models use scvi-tools.
not rated 113
+1 2mo ago A 79 tokens
Skill OpenCode
GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.
not rated 113
+1 2mo ago A 68 tokens
Skill OpenCode
Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble…
not rated 113
+1 2mo ago A 96 tokens
Skill OpenCode
Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker…
not rated 113
+1 2mo ago A 76 tokens
Skill OpenCode
ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene. Use to annotate variants with regulatory tracks, find open chromatin in…
not rated 113
+1 2mo ago A 128 tokens
Skill OpenCode
NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
not rated 113
+1 2mo ago A 72 tokens
Skill OpenCode
Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for…
not rated 113
+1 2mo ago A 105 tokens
Skill OpenCode
Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP. Scales to millions of cells. Python (harmonypy, scanpy) and R (Seurat).
not rated 113
+1 2mo ago A 63 tokens
Skill OpenCode
Open-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets. Integrates with Nextflow, Snakemake, W&B, scVI. For scRNA-seq use scanpy; for ontology lookups use bionty.
not rated 113
+1 2mo ago A 78 tokens
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