AlterLab-IEU

AlterLab-IEU/AlterLab-Academic-Skills

Plugin Claude Code

239 Claude skills for academic research, organized by domain.

AlterLab-IEU/AlterLab-Academic-Skills

Instructions file

Instructions for AlterLab-IEU/AlterLab-Academic-Skills, covering project overview, audience, naming convention, skill categories and core pipeline routing rules.

AlterLab-IEU/AlterLab-Academic-Skills

MCP server Claude CodeCodexCursor +2

The fast, Pythonic way to build MCP servers and clients. Runs locally from the fastmcp Python package.

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted structure with confidence metrics, ranking…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BLAST, or fetching records from Entrez …

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run cross-database analyses — for quick single-database lookups use gget, for…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parseseqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negativetaxids taxonomic scoping, and -mtmode multithreading; plus a DIAMOND blastp…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand, predicting a holo (ligand-bound)…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/peak heatmaps and profiles…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Run ESM protein language models — ESM3 for generative multimodal protein design across sequence, structure, and function, and ESM C for efficient embeddings and representations — locally or via the cloud Forge API. Use when working with protein sequences, structures, or function prediction, designing novel proteins…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting tree files, doing phylogenomic…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting channels and metadata, or preprocessing…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanced BLAST use biopython, for…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing therapeutic-antibody or biologic…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preprocessing — building tile datasets for ML…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or metal binding pocket, redesigning…

AlterLab-IEU/AlterLab-Academic-Skills

Skill Claude CodeCodex

Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when working with neural recordings, spike…