AlterLab-Academic-Skills

In the author's own words, from each skill's SKILL.md — showing the first 29 of 243 files.

• alterlab-alphafold

  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 models, or checking self-consistency of a design. For co-folding a protein WITH a…

  skills/bioinformatics/alterlab-alphafold/SKILL.md on GitHub (opens in a new tab)

• alterlab-anndata

  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 QC, normalization, clustering, UMAP, and differential-expression analysis pipeline…

  skills/bioinformatics/alterlab-anndata/SKILL.md on GitHub (opens in a new tab)

• alterlab-arboreto

  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 networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Pa…

  skills/bioinformatics/alterlab-arboreto/SKILL.md on GitHub (opens in a new tab)

• alterlab-biopython

  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 — for quick one-off database lookups use gget, for unified multi-service integrati…

  skills/bioinformatics/alterlab-biopython/SKILL.md on GitHub (opens in a new tab)

• alterlab-bioservices

  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 sequence and file manipulation use biopython. Part of the AlterLab Academic Ski…

  skills/bioinformatics/alterlab-bioservices/SKILL.md on GitHub (opens in a new tab)

• alterlab-blast

  Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs…

  skills/bioinformatics/alterlab-blast/SKILL.md on GitHub (opens in a new tab)

• alterlab-boltz

  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) complex or its binding affinity, or co-folding protein–DNA/RNA assemblies. For protei…

  skills/bioinformatics/alterlab-boltz/SKILL.md on GitHub (opens in a new tab)

• alterlab-borzoi

  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 non-coding/regulatory variant's effect on expression or chromatin, or doing in-s…

  skills/bioinformatics/alterlab-borzoi/SKILL.md on GitHub (opens in a new tab)

• alterlab-cellxgene

  Query the CZ CELLxGENE Census (200M+ 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 data against a reference — for analyzing your own dataset use scanpy or scvi-to…

  skills/bioinformatics/alterlab-cellxgene/SKILL.md on GitHub (opens in a new tab)

• alterlab-chai

  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, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or…

  skills/bioinformatics/alterlab-chai/SKILL.md on GitHub (opens in a new tab)

• alterlab-cobrapy

  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 metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab…

  skills/bioinformatics/alterlab-cobrapy/SKILL.md on GitHub (opens in a new tab)

• alterlab-deeptools

  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 (computeMatrix, plotHeatmap, plotProfile). Use for coverage tracks, signal heatmaps/profiles,…

  skills/bioinformatics/alterlab-deeptools/SKILL.md on GitHub (opens in a new tab)

• alterlab-esm

  Run ESM protein language models — ESMC for embeddings and representations, ESMFold2 for structure prediction, and ESM3 for generative multimodal protein design across sequence, structure, and function — locally or through the hosted Biohub Platform API (formerly Forge). Use when working with protein sequences, structures, or function prediction, designing novel proteins, generating protein embedd…

  skills/bioinformatics/alterlab-esm/SKILL.md on GitHub (opens in a new tab)

• alterlab-etetoolkit

  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 comparative analysis, or producing publication tree graphics in Python. Part of the Alter…

  skills/bioinformatics/alterlab-etetoolkit/SKILL.md on GitHub (opens in a new tab)

• alterlab-flowio

  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 cytometry data for downstream gating and analysis. Part of the AlterLab Academic Sk…

  skills/bioinformatics/alterlab-flowio/SKILL.md on GitHub (opens in a new tab)

• alterlab-gget

  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 multi-database Python workflows use bioservices. Part of the AlterLab Academic Skills suite.

  skills/bioinformatics/alterlab-gget/SKILL.md on GitHub (opens in a new tab)

• alterlab-glycoengineering

  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 glycoforms, or doing glycoprotein engineering and vaccine-design work. Part of the Al…

  skills/bioinformatics/alterlab-glycoengineering/SKILL.md on GitHub (opens in a new tab)

• alterlab-histolab

  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 training, tissue segmentation, or quick tile-based inspection of histopathology sl…

  skills/bioinformatics/alterlab-histolab/SKILL.md on GitHub (opens in a new tab)

• alterlab-lamindb

  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, diseases, tissues), tracking data lineage and computational workflows, building data la…

  skills/bioinformatics/alterlab-lamindb/SKILL.md on GitHub (opens in a new tab)

• alterlab-ligandmpnn

  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 residues that contact a ligand/ion/nucleic acid, or doing enzyme active-site design…

  skills/bioinformatics/alterlab-ligandmpnn/SKILL.md on GitHub (opens in a new tab)

• alterlab-neuropixels

  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 sorting, or extracellular electrophysiology, or when the user mentions Neuropixels,…

  skills/bioinformatics/alterlab-neuropixels/SKILL.md on GitHub (opens in a new tab)

• alterlab-nf-core-sarek

  Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.10.0 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR against the GATK GRCh38 resource bundle (dbSNP, Mills/1000G indels), and selects callers — explicitly correcting that sarek…

  skills/bioinformatics/alterlab-nf-core-sarek/SKILL.md on GitHub (opens in a new tab)

• alterlab-pathml

  Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 dataset management, and deep-learning model training on pathology data. Use when the user builds end-to-end deep-learning pat…

  skills/bioinformatics/alterlab-pathml/SKILL.md on GitHub (opens in a new tab)

• alterlab-phylogenetics

  Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstructing trees from sequences (FASTA) for evolutionary analysis, microbial genomics, viral phylodynamics, protein-family stu…

  skills/bioinformatics/alterlab-phylogenetics/SKILL.md on GitHub (opens in a new tab)

• alterlab-proteinmpnn

  Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inverse-folding a backbone PDB into sequences, redesigning selected positions, imposing symmetry across chains, or generati…

  skills/bioinformatics/alterlab-proteinmpnn/SKILL.md on GitHub (opens in a new tab)

• alterlab-pydeseq2

  Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially expressed genes between conditions from raw bulk RNA-seq counts. Part of the AlterLab Academic Skills suite.

  skills/bioinformatics/alterlab-pydeseq2/SKILL.md on GitHub (opens in a new tab)

• alterlab-pyopenms

  Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple spectral comparison and metabolite identification use matchms. Part of the AlterLab Academic Skills suite.

  skills/bioinformatics/alterlab-pyopenms/SKILL.md on GitHub (opens in a new tab)

• alterlab-pysam

  Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing pipelines that parse, filter, index, or compute coverage over BAM/CRAM/VCF files. Part of the AlterLab Academic Skills suite.

  skills/bioinformatics/alterlab-pysam/SKILL.md on GitHub (opens in a new tab)

• alterlab-qiime2-amplicon

  Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 distribution (2026.7; the "amplicon" distribution was renamed "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux quality .qzv), feature-classifier classify-sklearn against a version-matched SILVA 138 or Greengenes2 classifier, and di…

  skills/bioinformatics/alterlab-qiime2-amplicon/SKILL.md on GitHub (opens in a new tab)

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