Skill Claude CodeCodex
Cluster and phenotype high-dimensional flow/mass cytometry data to discover cell populations without predefined gates.
111 1mo ago A 27 tokens
Skill Claude CodeCodex
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).
111 1mo ago A 54 tokens
Skill Claude CodeCodex
Infer cis-regulatory peak-peak (and peak-gene) co-accessibility connections from scATAC data using Cicero, ArchR, or SCENIC+, with Hi-C concordance validation.
111 1mo ago A 47 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 58 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 50 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 49 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 49 tokens
Skill Claude CodeCodex
Read, write, create, merge, and convert single-cell data objects (AnnData/Scanpy and Seurat) for downstream analysis.
111 1mo ago A 34 tokens
Skill Claude CodeCodex
Sequence-based deep learning (chromBPNet, tangermeme, TF-MoDISco) for ATAC-seq: Tn5 bias correction, variant effect prediction, and de novo motif discovery.
111 1mo ago A 49 tokens
Skill Claude CodeCodex
Choose and produce publication-quality 2D dimensionality-reduction plots (PCA, t-SNE, UMAP, PHATE) with deliberate hyperparameters and honest interpretation limits.
111 1mo ago A 45 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 48 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 42 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 57 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 58 tokens
Skill Claude CodeCodex
Infer gene regulatory networks from single-cell data (pySCENIC for RNA-only, SCENIC+ for Multiome) and simulate TF perturbations with CellOracle.
111 1mo ago A 41 tokens
Skill Claude CodeCodex
Estimate SNP heritability and partition it across functional categories, cell types, and loci using LDSC, LDAK SumHer, HDL, and HESS.
111 1mo ago A 42 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 44 tokens
Skill Claude CodeCodex
Reconstruct cell lineage trees from CRISPR/lentiviral/mitochondrial barcodes and analyze clonal dynamics and fate decisions in single-cell lineage-tracing experiments.
111 1mo ago A 42 tokens
Skill Claude CodeCodex
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).
111 1mo ago A 44 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 46 tokens
Skill Claude CodeCodex
Infer metabolite-mediated cell-cell communication from scRNA-seq data using MeboCost, by predicting metabolite secretion from enzyme expression and sensing via receptors.
111 1mo ago A 39 tokens
Skill Claude CodeCodex
Compute per-sample/per-cell TF motif accessibility deviation z-scores with chromVAR (bulk, Signac, ArchR) and optionally refine TF activity with DecoupleR.
111 1mo ago A 42 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 59 tokens
Skill Claude CodeCodex
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.
111 1mo ago A 58 tokens