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Claude Skills by BioTender-max
github.com/BioTender-max897 skills8 installs817 views
- Wearable Analysis Agent--> --- name: wearable-analysis-agent description: Analyzes longitudinal wearable sensor data (heart rate, activity, sleep) to detect anomalies and provide personalized health insights. keywords: - wearable - sensor-data - health-monitoring - anomaly-detection - longitudinal-analysis measurable_outcome: Detects atrial fibrillation and sleep anomalies with >90% accuracy using continuous PPG and accelerometer data. license: MIT metadata: author: Biomedical AI Team version: "1.0.0" compatibility...Votes: 0GitHub stars: 171
- Wikipedia SearchSearch and fetch structured content from Wikipedia using the MediaWiki API for reliable, encyclopedic informationVotes: 0GitHub stars: 171
- Bio Image ProcessingSkills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.Votes: 0GitHub stars: 171
- Database AccessSkills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, processed functional-genomics tracks, Hi-C / Micro-C contact matrices, TCGA-style cohorts, and large-scale single-cell data.Votes: 0GitHub stars: 171
- Figure StylingAesthetic guidelines for scientific figure production. Each style file specifies palettes, typography, layout, and domain-specific sub-styles for a given target venue (NeurIPS, Nature, IEEE, etc.) and figure class (methodology diagram vs. statistical plot). Used by the Graph Maker Team's `illustrator` and `data_plotter` agents.Votes: 0GitHub stars: 171
- Gene Panel SelectionEnd-to-end workflow for gene panel design in scRNA-seq and spatial transcriptomics, that should be **STRICTLY** followed: dataset understanding + smart downsampling + train/test splits, algorithmic selection (HVG/DE/RF/scGeneFit/SpaPROS), optimal sub-panel discovery (ARI vs size), biological completion with a stability gate (Completion Rule), consensus scoring and completion (only if there is still room), and benchmarking on test splits (ARI/NMI/Silhouette + UMAP similarity).Votes: 0GitHub stars: 171
- General Data AnalysisGeneral-purpose skills for data analysis infrastructure: environment management, parallel computing, and performance optimization.Votes: 0GitHub stars: 171
- Live ViewSkills for opening and driving agent-controllable visualization components in the Pantheon UI sidebar — interactive viewers the agent can open, control, and read back. Viewers: Vitessce (spatial / single- cell omics), Viv (bioimage / microscopy), plus agent-generated apps.Votes: 0GitHub stars: 171
- NfcoreSkills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines.Votes: 0GitHub stars: 171
- OmicsSkills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.Votes: 0GitHub stars: 171
- OpenstSkills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.Votes: 0GitHub stars: 171
- Paper WritingSkills for the Paper Write Team: report and academic templates for HTML/PDF rendering. Each template file is self-contained (HTML + CSS or LaTeX in a single markdown file).Votes: 0GitHub stars: 171
- PresentationSkills for creating presentations, slides, and visual documentation.Votes: 0GitHub stars: 171
- Sc Best PracticesSkills derived from the Single-cell Best Practices book (sc-best-practices.org). Comprehensive workflows and guidelines for single-cell and spatial omics analysis.Votes: 0GitHub stars: 171
- ScfmWorkflow guidance and model reference for single-cell foundation models (scGPT, Geneformer, UCE, scBERT, etc.). Covers model selection, validation-first workflow, and per-model I/O contracts.Votes: 0GitHub stars: 171
- SegmentationCell and nucleus segmentation tools for microscopy images. Covers Cellpose, SAM-based methods, StarDist, InstanSeg, and Mesmer.Votes: 0GitHub stars: 171
- Single CellCore skills for single-cell RNA-seq analysis: quality control, cell type annotation, and trajectory inference. These are high-priority actionable workflows — load them first for common single-cell tasks.Votes: 0GitHub stars: 171
- SpatialSkills for spatial transcriptomics analysis including single-cell to spatial mapping (MOSCOT), 3D visualization (PyVista), and related spatial workflows.Votes: 0GitHub stars: 171
- Structural BiologyObtain and predict protein 3D structures — fetch AlphaFold predicted models from the AlphaFold DB, experimental structures from the RCSB PDB, or predict a novel sequence with ColabFold — and visualise them in the Mol* LiveView.Votes: 0GitHub stars: 171
- Upstream ProcessingSkills for upstream data processing in single-cell and spatial omics, covering raw data generation, barcode processing, alignment, spatial registration, and technology-specific preprocessing pipelines.Votes: 0GitHub stars: 171
- Archs4 DatabaseQuery ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).Votes: 0GitHub stars: 171
- Bioservices Multi DatabaseUnified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.Votes: 0GitHub stars: 171
- Cbioportal DatabaseCancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use dgidb-database.Votes: 0GitHub stars: 171
- Celltypist Cell AnnotationAutomated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker inspection.Votes: 0GitHub stars: 171
- Cnvkit Copy NumberDetect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use GATK CNV for deep WGS with population controls; use CNVkit for targeted/exome where antitarget bins matter.Votes: 0GitHub stars: 171
- Deeptools Ngs AnalysisNGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.Votes: 0GitHub stars: 171
- Deseq2 Differential ExpressionBulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.Votes: 0GitHub stars: 171
- Esm Protein Language ModelProtein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings. Design novel proteins, extract ML features, or fold sequences. Local GPU or EvolutionaryScale Forge API. Use AlphaFold for traditional folding; RDKit for small molecules.Votes: 0GitHub stars: 171
- Gseapy Gene EnrichmentGSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, GO, and 200+ databases; runs preranked GSEA on ranked DE gene lists. Outputs enrichment tables and running-score plots. Use after DESeq2 or edgeR for pathway-level interpretation.Votes: 0GitHub stars: 171
- Gwas DatabaseNHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.Votes: 0GitHub stars: 171
- Harmony Batch CorrectionHarmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP. Scales to millions of cells. Python (harmonypy, scanpy) and R (Seurat).Votes: 0GitHub stars: 171
- Lamindb Data ManagementOpen-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets. Integrates with Nextflow, Snakemake, W&B, scVI. For scRNA-seq use scanpy; for ontology lookups use bionty.Votes: 0GitHub stars: 171
- Latex Research PostersResearch posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure integration, accessibility, and QA for conferences. Includes templates. For figure generation use matplotlib-scientific-plotting or plotly-interactive-visualization.Votes: 0GitHub stars: 171
- Molfeat Molecular FeaturizationMolecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit 2D, Mordred), pretrained embeddings (ChemBERTa, GIN, Graphormer), pharmacophores. Scikit-learn compatible with parallelization/caching. For QSAR, virtual screening, similarity, and molecular DL.Votes: 0GitHub stars: 171
- Mouse Phenome DatabaseRetrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nomenclature or gene coordinates. Use for QTL support, cross-strain comparison, mouse model selection, and ontology-driven phenotype discovery. Use monarch-database for disease-gene-phenotype knowledge...Votes: 0GitHub stars: 171
- Networkx Graph AnalysisGraph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths, community detection, generators, I/O (GraphML, GML, edge list), matplotlib viz. For large graphs (100K+ nodes) use igraph or graph-tool; for GNNs use PyG.Votes: 0GitHub stars: 171
- Plink2 Gwas AnalysisGWAS and population genetics tool. Processes PLINK (.bed/.bim/.fam), VCF, and BGEN; runs QC (MAF, HWE, missingness), IBD estimation, PCA, and linear/logistic regression GWAS. Outputs Manhattan-ready summary stats. Use regenie or SAIGE for biobanks (>100k samples) needing mixed models.Votes: 0GitHub stars: 171
- Popv Cell AnnotationConsensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.Votes: 0GitHub stars: 171
- Protocolsio Integrationprotocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing. Public access free; auth needed for private or publishing. Pair with opentrons-integration or benchling-integration to execute.Votes: 0GitHub stars: 171
- Pydeseq2 Differential ExpressionBulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.Votes: 0GitHub stars: 171
- Scanpy Scrna SeqscRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.Votes: 0GitHub stars: 171
- Snpeff Variant AnnotationAnnotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl VEP for REST API; SnpEff for fast CLI with pre-built genomes.Votes: 0GitHub stars: 171
- Uniprot Protein DatabaseQuery UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database for structures.Votes: 0GitHub stars: 171
- Cancer MultiomicsIntegrated analysis of expression, mutation, copy number, and methylation data from TCGA and GEO for solid tumor characterization.Votes: 0GitHub stars: 171
- Immune DeconvolutionEstimate immune and stromal cell composition from bulk RNA-seq using multiple algorithms. Wraps CIBERSORT, quanTIseq, EPIC, xCell, MCP-counter, TIMER, and ESTIMATE through the immunedeconv unified interface.Votes: 0GitHub stars: 171
- Single Cell AtlasFull single-cell RNA-seq pipeline from raw counts to biological interpretation. Covers QC, normalization, batch integration, clustering, annotation, pseudobulk DE, trajectory inference, cell-cell communication, and TF activity. Dual-language: Seurat v5 (R) and scanpy (Python).Votes: 0GitHub stars: 171
- Survival AnalysisTime-to-event analysis for cancer clinical data. Covers Kaplan-Meier, Cox proportional hazards, competing risks, restricted mean survival time, and optimal cutpoint selection using the survival, ggsurvfit, tidycmprsk, and survRM2 packages.Votes: 0GitHub stars: 171