Research & Science

Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups…

GPTomics/bioSkills

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GETHOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs).

GPTomics/bioSkills

Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks.

GPTomics/bioSkills

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization…

GPTomics/bioSkills

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…

GPTomics/bioSkills

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGenfinder…

GPTomics/bioSkills

Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware…

GPTomics/bioSkills

Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens.

GPTomics/bioSkills

Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial…

GPTomics/bioSkills

Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions.

GPTomics/bioSkills

Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET…

GPTomics/bioSkills

Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP).

GPTomics/bioSkills

Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR…

GPTomics/bioSkills

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution.

GPTomics/bioSkills

Analyzes alternative splicing at single-cell resolution. An agent skill from GPTomics/bioSkills.

GPTomics/bioSkills

Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular…

GPTomics/bioSkills

Assesses RNA-seq data quality specifically for alternative splicing analysis.

GPTomics/bioSkills

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free…

GPTomics/bioSkills

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…

GPTomics/bioSkills

End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting.

GPTomics/bioSkills

Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart…

GPTomics/bioSkills

Clones and audits competitor repositories into evidence-based intelligence with file:line citations.

daymade/claude-code-skills

A skill your agent uses when Codex needs to evaluate novelty, closest related works, differentiators, and novelty-related rejection risks for a PaperPRISM project.

XueruiSu/Paper-PRISM

Check claim-to-evidence links, citation fields, conflicts, and unsupported language before writing a research brief.

Exekiel179/psyclaw

Patsnap Chemistry & Small Molecule MCP for AI agents. An agent skill from patsnap/mcp.

patsnap/mcp

Search and retrieve academic papers from arXiv using their free REST API.

AlexAI-MCP/hermes-CCC

Crisis communication and rapid-response workflows. An agent skill from jamditis/claude-skills-journalism.

jamditis/claude-skills-journalism

Structured fact-checking workflow. An agent skill from jamditis/claude-skills-journalism.

jamditis/claude-skills-journalism

the R package BioNAR, developed to step by step analysis of PPI network.

bioMate-AI/biomate-bioconductor-kb

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

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

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

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