Skill OpenCode
Cluster and phenotype high-dimensional flow/mass cytometry data to discover cell populations without predefined gates.
not rated 115 3mo ago A 27 tokens
Skill OpenCode
Single-cell clustering workflow: PCA dimensionality reduction, k-NN neighbor graph, Leiden/Louvain community detection, UMAP/tSNE embedding, and optional PAGA graph abstraction. Covers Scanpy (Python) and Seurat (R).
not rated 115 3mo ago A 54 tokens
Skill OpenCode
Infer cis-regulatory peak-peak (and peak-gene) co-accessibility connections from scATAC data using Cicero, ArchR, or SCENIC+, with Hi-C concordance validation.
not rated 115 3mo ago A 47 tokens
Skill OpenCode
Build weighted gene co-expression networks (WGCNA) to detect co-regulated gene modules, correlate them with sample traits, and identify hub genes; includes CEMiTool, hdWGCNA (single-cell), and PyWGCNA alternatives.
not rated 115 3mo ago A 58 tokens
Skill OpenCode
Analyze combinatorial CRISPR screens (Big Papi paired-Cas9 or in4mer/Inzolia Cas12a multiplex) to score synthetic-lethal and synthetic-rescue genetic interactions between gene pairs.
not rated 115 3mo ago A 50 tokens
Skill OpenCode
Build a tissue/condition-specific metabolic model by constraining a generic genome-scale model with transcriptomics data using GIMME, iMAT, or GTEx-based tissue extraction, then validate against the original model.
not rated 115 3mo ago A 49 tokens
Skill OpenCode
End-to-end pooled and single-cell CRISPR screen pipeline: library validation, guide counting, six-stage QC, copy-number/batch correction, design-matched hit calling, and tier-based consensus.
not rated 115 3mo ago A 49 tokens
Skill OpenCode
Read, write, create, merge, and convert single-cell data objects (AnnData/Scanpy and Seurat) for downstream analysis.
not rated 115 3mo ago A 34 tokens
Skill OpenCode
Sequence-based deep learning (chromBPNet, tangermeme, TF-MoDISco) for ATAC-seq: Tn5 bias correction, variant effect prediction, and de novo motif discovery.
not rated 115 3mo ago A 49 tokens
Skill OpenCode
Choose and produce publication-quality 2D dimensionality-reduction plots (PCA, t-SNE, UMAP, PHATE) with deliberate hyperparameters and honest interpretation limits.
not rated 115 3mo ago A 45 tokens
Skill OpenCode
Identify differentially methylated regions (DMRs) from WGBS or methylation-array data using tiling, smoothing, or kernel-based approaches, then refine, annotate, visualize, and export them.
not rated 115 3mo ago A 48 tokens
Skill OpenCode
Detect and remove cell doublets from flow cytometry or CyTOF data using scatter gating, DNA/event-length methods, or regression residuals, with batch processing and visualization.
not rated 115 3mo ago A 42 tokens
Skill OpenCode
Predict which gene a distal accessible (enhancer) region regulates by combining accessibility activity, 3D contact frequency, and sequence features into a per-(enhancer, gene) score; validate with CRISPRi-FlowFISH.
not rated 115 3mo ago A 57 tokens
Skill OpenCode
Detect and remove cell doublets/aggregates from flow cytometry or CyTOF data using scatter gating, automated/QC methods, regression/ratio scoring, and CyTOF DNA/event-length detection, before clustering or quantitative analysis.
not rated 115 3mo ago A 58 tokens
Skill OpenCode
Infer gene regulatory networks from single-cell data (pySCENIC for RNA-only, SCENIC+ for Multiome) and simulate TF perturbations with CellOracle.
not rated 115 3mo ago A 41 tokens
Skill OpenCode
Estimate SNP heritability and partition it across functional categories, cell types, and loci using LDSC, LDAK SumHer, HDL, and HESS.
not rated 115 3mo ago A 42 tokens
Skill OpenCode
Interactively annotate cell types in multiplexed imaging (IMC) data using napari visualization with marker overlays, then extract training data, propagate labels with KNN, and validate annotations.
not rated 115 3mo ago A 44 tokens
Skill OpenCode
Reconstruct cell lineage trees from CRISPR/lentiviral/mitochondrial barcodes and analyze clonal dynamics and fate decisions in single-cell lineage-tracing experiments.
not rated 115 3mo ago A 42 tokens
Skill OpenCode
Find differentially expressed marker genes per cluster, visualize them, score gene sets/cell cycle, and manually annotate cell types. Supports Scanpy (Python) and Seurat (R).
not rated 115 3mo ago A 44 tokens
Skill OpenCode
Build publication-ready figures in Python with matplotlib's object-oriented Figure/Axes API, seaborn integration, Type-42 fonts, CVD-safe palettes, and rasterized point layers.
not rated 115 3mo ago A 46 tokens
Skill OpenCode
Infer metabolite-mediated cell-cell communication from scRNA-seq data using MeboCost, by predicting metabolite secretion from enzyme expression and sensing via receptors.
not rated 115 3mo ago A 39 tokens
Skill OpenCode
Compute per-sample/per-cell TF motif accessibility deviation z-scores with chromVAR (bulk, Signac, ArchR) and optionally refine TF activity with DecoupleR.
not rated 115 3mo ago A 42 tokens
Skill OpenCode
Jointly analyze multimodal single-cell data (CITE-seq RNA+protein, 10X Multiome RNA+ATAC) using Weighted Nearest Neighbors (WNN) or Multi-Omics Factor Analysis (MOFA) integration.
not rated 115 3mo ago A 59 tokens
Skill OpenCode
Complete 10X Multiome (joint scRNA + scATAC) analysis workflow using Seurat and Signac: load joint data, modality-specific QC and dimensionality reduction, WNN integration, clustering, markers, and gene-peak linkage.
not rated 115 3mo ago A 58 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: