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SkillsMP has collected 236 skills from BioTender-max/awesome-bio-agent-skills. Open a skill to review its source and details.
BioTender-max/awesome-bio-agent-skillsShowing 40 of 236 collected skills.
Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and…
Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between…
Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and…
Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket),…
Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal…
Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast…
Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT…
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
Cell segmentation in fluorescence microscopy images. Supports Cellpose/cpsam (Cellpose 4.0) with additional backends planned. Produces segmentation masks, per-cell morphology metrics (area, diameter, centroid, eccentricity), overlay figures, and a report.md.
Deterministic CRISPR screen hit ranking from local guide-level count tables
Summarise pre-computed differential expression results with ranked gene lists, biological themes, and publication-ready interpretation.
Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP. Use when an agent needs GWAS beta / SE / p-value for every variant in a window for one specific study (GCST accession). Input: accession,…
Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.
Wrapper skill for running nf-core/scrnaseq upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
Compute organ-specific biological age from Olink proteomic data using Goeminne et al. (2025) elastic net aging clocks.
Browser automation via agent-browser CLI for web navigation, form filling, screenshots, scraping, login flows, and UI testing.
Critically review, score, compare, and rank one or more AI scientist outputs for biology, bioinformatics, computational life science, or adjacent research tasks. Trigger when the user asks to evaluate notebooks, code, figures, analyses, manuscripts, software,…
Search arXiv preprints through the official arXiv API and turn arXiv IDs into local Markdown summaries. Use when you need CS, math, physics, or quantitative biology preprints, especially recent submissions that may not yet appear in peer-reviewed literature…
Create publication-quality matplotlib/seaborn charts with readable axes, tight layout, and curated palettes.
Functional annotation and taxonomy inference from sequence homology.
Assemble genomes/metagenomes and produce assembly QC artifacts.
Perform metagenomic binning with QuickBin, refinement, and QC with completeness/contamination checks.
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.
Build marker gene alignments and phylogenetic trees.
Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.
Cluster proteins into orthogroups and derive pangenome matrices.
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
Aggregate results, train ML models, and produce reports with validated references.
Structure prediction and structure-based annotation.
Detect, classify, and QC viral contigs.
Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.
Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries. Use when you need recent biology preprints, bioRxiv-native metadata, date-range scans, DOI lookups, or author shortlists that may…
Query the Crossref REST API for DOI validation, title search, citation metadata, and bibliography audits. Use when you need DOI lookup, title-to-DOI matching, or reference metadata cleanup.
Fetch current API and SDK documentation with the chub CLI. Use when writing or reviewing code against fast-changing APIs, especially when the user asks for the latest or current docs.
Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Downloads genome files from JGI filesystem using IMG taxon OIDs and links JGI taxon OIDs to read files through PMO/GOLD identifiers and JAMO. Use when working with JGI…