Alternatives to arrayexpress-fetch
arrayexpress-fetch is an agent skill by Nikolai Hecker, UK Dementia Research Institute: Query metadata and download data from ArrayExpress, EMBL-EBI's functional genomics collection, now hosted inside BioStudies. If it doesn't fit your setup, these 12 agent skills cover similar ground. They are ordered by how closely they match arrayexpress-fetch and by our rank, which weighs adoption, freshness and documentation; money never changes the order. complexa-target leads the list (larger repository (3.7K stars)). Each entry shows data reasons to switch, and you can open a side-by-side comparison with arrayexpress-fetch.
Updated Oct 26, 2026 · Built from catalog data; how we rank and grade
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arrayexpress-fetch
Query metadata and download data from ArrayExpress, EMBL-EBI's functional genomics collection, now hosted inside BioStudies.
12 alternatives
Ordered by how closely each matches arrayexpress-fetch (shared product, category or stated alternative) and by rank.
- 1complexa-target
Ohad Mosafi <omosafi@nvidia.com>
Add, edit, inspect, or validate Proteina-Complexa target definitions for protein binders, ligand binders, and AME motif scaffolding.
- Larger repository (3.7K stars)
★ 3.7KLast active Oct 21, 2026Claude Code, Claude apps, Codex, Cursor +6
AFreshness: A–Security: not graded yet - 2rfd4-proteina-nim
NVIDIA BioNeMo <bionemofeedback@nvidia.com>
Run RFD4-Proteina NIM for joint protein structure and sequence design, conditioned generation, and reward-guided search using the NVIDIA hosted API or a…
- Larger repository (3.7K stars)
★ 3.7KLast active Oct 21, 2026Claude Code
AFreshness: A–Security: not graded yet - 3article-data-fetcher
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…
- Repository has 1.2K stars
- Active in the last 30 days
★ 1.2KLast active Oct 11, 2026Claude Code, Claude apps, Codex, Cursor +6
AFreshness: A–Security: not graded yet - 4nvmolkit-usage
Kevin Boyd (@scal444)
Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.
- Larger repository (3.7K stars)
★ 3.7KLast active Sep 23, 2026Claude Code, Claude apps, Codex, Cursor +6
BFreshness: B–Security: not graded yet - 5scrna-orchestrator
Yonghao Zhao
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent…
- Repository has 1.2K stars
- Open source (MIT)
★ 1.2KLast active Sep 11, 2026Claude Code, Claude apps, Codex, Cursor +6
BFreshness: B–Security: not graded yet - 6analyze-fasta
Santiago Rodriguez Salinas
Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython…
- Repository has 1.2K stars
- Open source (MIT)
★ 1.2KLast active Sep 17, 2026Claude Code, Claude apps, Codex, Cursor +6
BFreshness: B–Security: not graded yet - 7repro-enforcer
ClawBio
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
- Repository has 1.2K stars
- Open source (MIT)
★ 1.2KLast active Sep 11, 2026Claude Code, Claude apps, Codex, Cursor +6
BFreshness: B–Security: not graded yet - 8polars-bio
ClawBio (adapted from K-Dense scientific-agent-skills/polars-bio)
Fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O…
- Repository has 1.2K stars
- Active in the last 30 days
★ 1.2KLast active Sep 25, 2026Claude Code, Claude apps, Codex, Cursor +6
AFreshness: A–Security: not graded yet - 9rare-high-impact-variants
Manuel Corpas
Count rare, high-impact loss-of-function variants carried in a VCF, annotated with molecular consequence and population allele frequency
- Repository has 1.2K stars
- Active in the last 30 days
★ 1.2KLast active Oct 19, 2026Claude Code, Claude apps, Codex, Cursor +6
AFreshness: A–Security: not graded yet - 10organ-aging-studio
ClawBio hackathon contributor
Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient).
- Repository has 1.2K stars
- Active in the last 30 days
★ 1.2KLast active Oct 19, 2026Claude Code, Claude apps, Codex, Cursor +6
AFreshness: A–Security: not graded yet - 11lit-synthesizer
Sooraj (github.com/sooraj-codes)
Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a…
- Repository has 1.2K stars
- Active in the last 30 days
★ 1.2KLast active Oct 20, 2026Claude Code, Claude apps, Codex, Cursor +6
AFreshness: A–Security: not graded yet - 12celltype-specificity-profiler
Jacky Siu
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…
- Repository has 1.2K stars
- Active in the last 30 days
★ 1.2KLast active Oct 19, 2026Claude Code, Claude apps, Codex, Cursor +6
AFreshness: A–Security: not graded yet