Skill OpenCode
Deduplicate UMI-tagged sequencing reads: extract UMIs from FASTQ, align, collapse PCR duplicates, and count molecules per gene/cell using UMI-tools.
not rated 115 3mo ago A 40 tokens
Skill OpenCode
Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast results.
not rated 115 3mo ago A 30 tokens
Skill OpenCode
Run upstream single-cell RNA-seq preprocessing from raw FASTQ to .h5ad using the nf-core/scrnaseq Nextflow pipeline, with strict preflight, six aligner presets, provenance, and downstream handoff.
not rated 115 3mo ago A 58 tokens
Skill OpenCode
Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input.
not rated 115 3mo ago A 38 tokens
Skill OpenCode
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional.
not rated 115 3mo ago A 33 tokens
Skill OpenCode
Query the OpenTargets Platform GraphQL API for drug-target-disease associations, therapeutic evidence, and clinical drug metadata. Use when users ask about drug targets for a disease, disease-gene associations, drugs targeting a specific gene, or evidence for target validation.
not rated 115 3mo ago A 57 tokens
Skill OpenCode
Access the UniProt REST API locally for protein sequence retrieval, annotation/domain extraction, entry search, PDB cross-references, and variant cataloging.
not rated 115 3mo ago A 36 tokens
debug-conda
80Skill OpenCode
Diagnose and repair conda environment errors.
not rated 115 3mo ago A 13 tokens
Skill OpenCode
Diagnose and repair missing input or reference files.
not rated 115 3mo ago A 15 tokens
Skill OpenCode
Diagnose and repair missing Python package.
not rated 115 3mo ago A 12 tokens
Skill OpenCode
Diagnose and repair reference genome or annotation mismatch.
not rated 115 3mo ago A 15 tokens
Skill OpenCode
Diagnose and repair missing CLI tool.
not rated 115 3mo ago A 13 tokens
Skill OpenCode
Define scRNA-seq input requirements and generic analysis conventions.
not rated 115 3mo ago A 19 tokens
Skill OpenCode
Define tumor research modes and route tumor scRNA-seq pipelines.
not rated 115 3mo ago A 19 tokens
Skill OpenCode
Python conda environment for scRNA-seq tools.
not rated 115 3mo ago A 18 tokens
env-r-bioc
88Skill OpenCode
R/Bioconductor environment for auxiliary oncology plots.
not rated 115 3mo ago A 16 tokens
Skill OpenCode
Bulk ATAC-seq processing: assay QC gates, MACS3 fragment-aware peak calling, consensus peak matrices, differential accessibility, and motif/footprint follow-up.
not rated 115 3mo ago A 42 tokens
exec-cnmf
90Skill OpenCode
Run cNMF co-expression module analysis.
not rated 115 3mo ago A 14 tokens
Skill OpenCode
Run inferCNVpy malignant cell identification.
not rated 115 3mo ago A 16 tokens
Skill OpenCode
Run Palantir state trajectory analysis.
not rated 115 3mo ago A 13 tokens
exec-scanpy
93Skill OpenCode
Run Scanpy QC, preprocessing, clustering, and annotation steps.
not rated 115 3mo ago A 18 tokens
Skill OpenCode
Shotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible cohort-ready output tables.
not rated 115 3mo ago A 39 tokens
Skill OpenCode
Spatially informed clustering of spatial transcriptomics data into spatial domains using GraphST (graph self-supervised contrastive learning + GNN).
not rated 115 3mo ago A 34 tokens
Skill OpenCode
Spatial domain identification with GreS, a semantic-guided spatial representation learning framework that injects gene-level functional priors into GCN-based spot embeddings and clusters them with k-means.
not rated 115 3mo ago A 44 tokens
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: