Skill Claude CodeCodex
Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
not rated 112
+1 1mo ago A 36 tokens
112Stars on the repository
200Mods indexed here, across every type
1mo agoLast push, which is what freshness is scored on
noneNo LICENSE: all rights reserved, so bodies are not copied
Skill Claude CodeCodex
Ligand-receptor communication inference in single-cell or spatial data with sender-receiver summaries and cautious interpretation.
not rated 112
+1 1mo ago A 30 tokens
Skill Claude CodeCodex
Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation.
not rated 112
+1 1mo ago A 33 tokens
Skill Claude CodeCodex
Workflow for spatial transcriptomics preprocessing, domain detection, deconvolution, neighborhood analysis, and publication-ready spatial maps.
not rated 112
+1 1mo ago A 34 tokens
Skill Claude CodeCodex
Pseudotime, lineage branching, and state-transition analysis for single-cell data with coherent embeddings and annotations.
not rated 112
+1 1mo ago A 32 tokens
Skill Claude CodeCodex
Standard scRNA-seq preprocessing and clustering with Scanpy: QC, filtering, normalization, HVG selection, PCA, neighbors, UMAP, and Leiden clustering, producing an analysis-ready AnnData object.
not rated 112
+1 1mo ago A 52 tokens
Skill Claude CodeCodex
Router/index skill over 1,676 deduplicated biomedical AI agent skills aggregated from 20 repositories into 15 categories; use it to search the index, locate the best-matching skill, fetch its SKILL.md on demand, and follow it.
not rated 112
+1 1mo ago A 62 tokens
Skill Claude CodeCodex
End-to-end protein binder design via BindCraft AF2 hallucination with built-in validation; runs on Modal or locally and reports per-design QC metrics.
not rated 112
+1 1mo ago A 35 tokens
biomaster
09Skill Claude CodeCodex
Load BioMaster as one integrated skill-driven bioinformatics assistant.
not rated 112
+1 1mo ago A 16 tokens
Skill Claude CodeCodex
Map query scRNA-seq data onto a pre-trained reference atlas via scArches surgical transfer learning (scVI/scANVI) to obtain a shared latent embedding and transferred cell type labels without retraining the reference.
not rated 112
+1 1mo ago A 51 tokens
Skill Claude CodeCodex
Integrate multiple scRNA-seq batches to remove batch effects while preserving biological variation, using Harmony, scVI, Seurat anchors, or fastMNN.
not rated 112
+1 1mo ago A 39 tokens
Skill Claude CodeCodex
Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) into a BioMaster project's bioskills library.
not rated 112
+1 1mo ago A 35 tokens
Skill Claude CodeCodex
Detect and remove doublets from scRNA-seq data using Scrublet (Python), DoubletFinder (R), or scDblFinder (R).
not rated 112
+1 1mo ago A 44 tokens
Skill Claude CodeCodex
Automated cell type annotation for preprocessed single-cell data using reference-based and custom classifiers (CellTypist, SingleR, Azimuth, scPred), with confidence filtering, consensus voting, and marker-based validation.
not rated 112
+1 1mo ago A 49 tokens
Skill Claude CodeCodex
Infer and quantify cell-cell communication from scRNA-seq data using CellChat, NicheNet, and LIANA frameworks.
not rated 112
+1 1mo ago A 31 tokens
Skill Claude CodeCodex
Segment cells from IMC images using Cellpose/Mesmer/steinbock and extract per-cell expression data with spatial coordinates.
not rated 112
+1 1mo ago A 33 tokens
Skill Claude CodeCodex
Integrate multiple histone modification ChIP-seq tracks into chromatin states via ChromHMM (with alternatives Segway, EpiSegMix, IDEAS, EpiLogos, full-stack ChromHMM).
not rated 112
+1 1mo ago A 54 tokens
Skill Claude CodeCodex
Cluster and phenotype high-dimensional flow/mass cytometry data to discover cell populations without predefined gates.
not rated 112
+1 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).
not rated 112
+1 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.
not rated 112
+1 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.
not rated 112
+1 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.
not rated 112
+1 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.
not rated 112
+1 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.
not rated 112
+1 1mo ago A 49 tokens
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