alterlab-geo
From the author
Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-geo -a claude-code
Installs to .claude/skills/alterlab-geo/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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Similar skills
Closest to this one by what they do and when they are used.
- geo-databasejaechang-hits/SciAgent-SkillsNCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.Data★ 383
- alterlab-gene-dbAlterLab-IEU/AlterLab-Academic-SkillsQuery NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.Science★ 78
- alterlab-enaAlterLab-IEU/AlterLab-Academic-SkillsAccess the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.Science★ 78
- alterlab-gtexAlterLab-IEU/AlterLab-Academic-SkillsQuery the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across 54 human tissues), expression QTLs (eQTLs), and splicing QTLs (sQTLs). Use when checking which tissues express a gene, finding which gene a non-coding/GWAS variant regulates via eQTLs, or interpreting variant regulatory effects across tissues. NOT for curated trait-variant associations (use alterlab-gwas), population allele frequencies or variant constraint (use alterlab-gnomad), or gene/transcript structure and ID mapping (use alterlab-ensembl). Part of the AlterLab Academic Skills suite.Legal★ 78
- alterlab-gtarsAlterLab-IEU/AlterLab-Academic-SkillsRuns high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the performance-critical backend for the geniml ML library. Use when computing overlaps/jaccard/coverage between BED region sets, indexing intervals with IGD, generating uniwig accumulation/coverage tracks, tokenizing genomic regions for ML, splitting single-cell fragments into pseudobulks, or computing GA4GH refget sequence digests. NOT for training region embeddings (use alterlab-geniml) or non-genomic spatial joins (use alterlab-geopandas). Part of the AlterLab Academic Skills suite.Science★ 78
- alterlab-gwasAlterLab-IEU/AlterLab-Academic-SkillsQuery the NHGRI-EBI GWAS Catalog REST API v2 for curated SNP-trait associations, retrieving variants by rs ID, disease/trait (EFO/MONDO), gene, or study (GCST) with p-values, effect sizes, and ancestry, and locate full harmonised summary statistics on the FTP site. Use when investigating genome-wide association study hits, mapping a SNP or rsID to traits, selecting GWAS for polygenic risk scores or fine-mapping, or doing genetic epidemiology lookups. Part of the AlterLab Academic Skills suite.Science★ 78
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