A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences. Use when integrating multiple scRNA-seq batches or datasets.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing data across batches.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Calculates species richness, diversity, and turnover using the Hill number framework with iNEXT coverage-based rarefaction/extrapolation, asymptotic diversity estimation, and beta diversity partitioning (betapart turnover vs nestedness). Compares assemblages using coverage-standardized rather than size-standardized…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use when identifying biomarkers from high-dimensional omics data.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV, and SHAP interpretation. Use when building and validating diagnostic or prognostic biomarker signatures from omics data.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival models from clinical and omics features. Use when predicting patient survival or modeling time-to-event outcomes.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and DEqMS workflows with empirical Bayes moderation, fold change shrinkage for accurate effect size estimation, and Python alternatives. Use when identifying proteins with…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the maxtargetseqs trap…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: