Skill OpenCode
Analyze single-cell ATAC-seq data: QC, LSI dimensionality reduction, clustering, peak calling, and motif activity scoring.
not rated 113
+1 2mo ago A 34 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
Skill OpenCode
Infer transcription factor regulons from scRNA-seq with the pySCENIC three-step pipeline (GRNBoost2 → cisTarget → AUCell) plus downstream interpretation.
not rated 113
+1 2mo ago A 44 tokens
Skill OpenCode
Analyze single-cell TCR/BCR immune receptor data with scRNA-seq gene expression using scirpy for joint clonotype and cell-state analysis.
not rated 113
+1 2mo ago A 37 tokens
Skill OpenCode
Complete single-cell RNA-seq workflow from 10X Cell Ranger counts to annotated cell types, with parallel Seurat (R) and scanpy (Python) paths.
not rated 113
+1 2mo ago A 43 tokens
Skill OpenCode
Process 10X scATAC / Multiome data from cellranger output to clustered, annotated cells with per-cluster peaks; choose Signac / ArchR / SnapATAC2 by language and scale.
not rated 113
+1 2mo ago A 50 tokens
Skill OpenCode
Detect and remove doublets from scRNA-seq data using Scrublet, DoubletFinder, or scDblFinder.
not rated 113
+1 2mo ago A 35 tokens
Skill OpenCode
Single-cell alternative splicing analysis: chemistry gating, junction quantification, per-cell PSI estimation with modality classification, differential splicing / cell-state association testing, APA pivot for 10X 3' data, and quality control with failure-mode reconciliation.
not rated 113
+1 2mo ago A 57 tokens
Skill OpenCode
Memory-efficient storage, manipulation, and normalization of zero-heavy (single-cell) expression matrices using scipy.sparse and AnnData.
not rated 113
+1 2mo ago A 32 tokens
Skill OpenCode
Analyze spatial cell-cell interactions in multiplexed imaging (IMC) data using squidpy: build spatial neighborhood graphs, test interaction enrichment, characterize local microenvironments, identify spatial domains, and visualize/export results.
not rated 113
+1 2mo ago A 48 tokens
Skill OpenCode
Estimate cell-type composition in spatial transcriptomics spots using an annotated scRNA-seq reference (cell2location primary; Tangram and RCTD alternatives).
not rated 113
+1 2mo ago A 39 tokens
Skill OpenCode
Identify spatial domains (tissue regions) in spatial transcriptomics data by combining gene expression with spatial proximity, then refine, evaluate, and annotate them.
not rated 113
+1 2mo ago A 37 tokens
Skill OpenCode
Visualize spatial transcriptomics data: overlay gene expression, clusters, QC metrics, and spatial statistics on tissue coordinates with optional histology background, interactive napari views, and publication-quality figures.
not rated 113
+1 2mo ago A 46 tokens
Skill OpenCode
Download and verify FASTQ from SRA/ENA accessions, with metadata resolution, single-cell/10x technical-read handling, and cloud (STRIDES) support.
not rated 113
+1 2mo ago A 40 tokens
Skill OpenCode
Profile RBP-RNA targets without UV crosslinking or immunoprecipitation using deaminase-RBP fusions (STAMP/TRIBE/DART-seq); recover RBP-specific editing sites computationally from bulk RNA-seq or scRNA-seq by subtracting a deaminase-only control.
not rated 113
+1 2mo ago A 70 tokens
Skill OpenCode
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.
not rated 113
+1 2mo ago A 39 tokens
Skill OpenCode
Infer developmental trajectories and pseudotime ordering from single-cell data using Monocle3, Slingshot, scVelo, PAGA, and velocyto.
not rated 113
+1 2mo ago A 40 tokens
Skill OpenCode
Fit smooth non-linear curves to gene expression time series using GAMs (mgcv/tradeSeq), test for temporal trends and condition differences, detect abrupt changepoints (segmented/ruptures), and visualize fitted trajectories with confidence intervals.
not rated 113
+1 2mo ago A 55 tokens
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 113
+1 2mo ago A 40 tokens
Skill OpenCode
Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast results.
not rated 113
+1 2mo 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 113
+1 2mo 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 113
+1 2mo ago A 38 tokens
Skill OpenCode
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional.
not rated 113
+1 2mo 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 113
+1 2mo 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 113
+1 2mo ago A 36 tokens
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