By ClawBio

Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output.

ClawBio/ClawBio

Blood RNA-seq expression-outlier detection for rare-disease diagnostics.

ClawBio/ClawBio

Produce offspring genomes from parent pairs via meiotic recombination, mutation, and clinical evaluation

ClawBio/ClawBio

Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.

ClawBio/ClawBio

Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from…

ClawBio/ClawBio

NGS read QC, alignment, and BAM processing pipeline. An agent skill from ClawBio/ClawBio.

ClawBio/ClawBio

Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json

ClawBio/ClawBio

Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns

ClawBio/ClawBio

Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning.

ClawBio/ClawBio

Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.

ClawBio/ClawBio

Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD.

ClawBio/ClawBio

Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.

ClawBio/ClawBio

Generates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation, pharmacogenomic alerts, and follow-up recommendations.

ClawBio/ClawBio

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.

ClawBio/ClawBio

Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.

ClawBio/ClawBio

Aggregate public target-level evidence across omics and translational sources for research triage.

ClawBio/ClawBio

Protein structure prediction with Boltz-2 (default) or OpenFold3.

ClawBio/ClawBio

Given an article DOI or PubMed ID, discover and download the genomics data files deposited by the authors (VCF, FASTA, H5AD, CSV, JSON, BAM, etc.) from public repositories such as GEO, ENA, Zenodo…

ClawBio/ClawBio

Run read-only SQL against BigQuery public datasets with local result capture, cost safeguards, and reproducibility outputs.

ClawBio/ClawBio

Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation.

ClawBio/ClawBio

Genome, transcriptome, and protein completeness assessment via BUSCO v6.

ClawBio/ClawBio

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the…

ClawBio/ClawBio

Methylation cycle analysis — enzymatic activity profiles, Net Methylation Capacity, BH4 axis estimates, compound heterozygosity detection from SNP genotype data.

ClawBio/ClawBio

Eval-driven skill tuning. An agent skill from ClawBio/ClawBio.

ClawBio/ClawBio

Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance…

ClawBio/ClawBio

Classify structural variants / copy-number variants (deletions and duplications) using the ClinGen / ACMG 2019 (Riggs et al.

ClawBio/ClawBio

Extract numerical data from scientific figure images using Claude vision + OpenCV calibration.

ClawBio/ClawBio

Objective-driven pooled viability screen analysis: QC, hit calling, context-selectivity, biomarker sweep, and ranked repurposing candidates.

ClawBio/ClawBio

Predict gene and transcript structure (intervals, exons, strand) from a DNA sequence using the Genomic Intelligence DNA Annotation model, via the hosted /v1/tasks/annotation/predict API.

ClawBio/ClawBio

Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.

ClawBio/ClawBio

Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API.

ClawBio/ClawBio

Predict tissue / cell-type expression (log TPM + TPM) from 9,198–500,000 bp of DNA around a TSS, at least 4,599 bp each side (anything but exactly 9,198 bp needs --tss-index) using the Genomic…

ClawBio/ClawBio

Detect promoter regions in DNA sequences using the Genomic Intelligence G0 transformer (GENA-LM BERT Large), via the hosted /v1/tasks/promoter/predict API.

ClawBio/ClawBio

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API.

ClawBio/ClawBio

Compute evidence-aware polygenic risk scores from a local VCF or WGS file through the validated just-prs engine and a pinned local just-prs MCP server.

ClawBio/ClawBio

Query and display Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy.

ClawBio/ClawBio

Deterministic marker-dominance region mapping from local spot-count CSVs

ClawBio/ClawBio

Wrapper skill for running nf-core/rnastructurome — chemical-probing RNA structure analysis (SHAPE/DMS, RT-stop/MaP readout) from FASTQ to per-base reactivity, secondary-structure predictions, and 2D…

ClawBio/ClawBio

Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient).

ClawBio/ClawBio

Gene-set pathway enrichment analysis using Enrichr — queries KEGG, GO (BP/MF/CC), Reactome, WikiPathways, MSigDB, and Disease Ontology.

ClawBio/ClawBio

End-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.

ClawBio/ClawBio

Search PubMed, preserve complete abstracts and sections, and produce research briefings with abstract openings or optional OpenAI/Ollama summaries.

ClawBio/ClawBio

Count rare, high-impact loss-of-function variants carried in a VCF, annotated with molecular consequence and population allele frequency

ClawBio/ClawBio

Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers

ClawBio/ClawBio

Analyse 10x Visium spatial transcriptomics: SpaceRanger outs or spatial h5ad in, then QC, Leiden clustering, Wilcoxon markers, Moran's I, neighbourhood enrichment and co-occurrence in one local…

ClawBio/ClawBio

Query metadata and download data from EMBL-EBI BioStudies, the database that describes biological studies and links their data across collections (ArrayExpress, BioImages, BioModels, EGA-linked…

ClawBio/ClawBio

Query metadata and download sequencing data from the European Nucleotide Archive (ENA) via the Portal and Browser APIs.

ClawBio/ClawBio

Query metadata and download data from the NCBI Gene Expression Omnibus (GEO).

ClawBio/ClawBio