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SkillsMP a collecté 236 skills depuis BioTender-max/awesome-bio-agent-skills. Ouvrez un skill pour examiner sa source et ses détails.
BioTender-max/awesome-bio-agent-skillsAffichage de 40 skills collectés sur 236.
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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),…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
Langue du texte source : anglais
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.
Langue du texte source : anglais
Deterministic CRISPR screen hit ranking from local guide-level count tables
Langue du texte source : anglais
Summarise pre-computed differential expression results with ranked gene lists, biological themes, and publication-ready interpretation.
Langue du texte source : anglais
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,…
Langue du texte source : anglais
Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
Langue du texte source : anglais
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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.
Langue du texte source : anglais
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
Langue du texte source : anglais
Compute organ-specific biological age from Olink proteomic data using Goeminne et al. (2025) elastic net aging clocks.
Langue du texte source : anglais
Browser automation via agent-browser CLI for web navigation, form filling, screenshots, scraping, login flows, and UI testing.
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
Create publication-quality matplotlib/seaborn charts with readable axes, tight layout, and curated palettes.
Langue du texte source : anglais
Functional annotation and taxonomy inference from sequence homology.
Langue du texte source : anglais
Assemble genomes/metagenomes and produce assembly QC artifacts.
Langue du texte source : anglais
Perform metagenomic binning with QuickBin, refinement, and QC with completeness/contamination checks.
Langue du texte source : anglais
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
Langue du texte source : anglais
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
Langue du texte source : anglais
Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.
Langue du texte source : anglais
Build marker gene alignments and phylogenetic trees.
Langue du texte source : anglais
Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.
Langue du texte source : anglais
Cluster proteins into orthogroups and derive pangenome matrices.
Langue du texte source : anglais
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
Langue du texte source : anglais
Aggregate results, train ML models, and produce reports with validated references.
Langue du texte source : anglais
Structure prediction and structure-based annotation.
Langue du texte source : anglais
Detect, classify, and QC viral contigs.
Langue du texte source : anglais
Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.
Langue du texte source : anglais
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…
Langue du texte source : anglais
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.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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…
Langue du texte source : anglais