gwas-lookup
Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.
2.85k repo starsObserved in 11 repos
Research
Research skills
Browse reusable Agent Skills, each with a clear purpose and practical guidance.
binder-design
Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
2.85k repo starsObserved in 10 repos
Research
bio-de-edger-basics
Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.
2.85k repo starsObserved in 10 repos
Research
bio-metagenomics-kraken
Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.
2.85k repo starsObserved in 10 repos
Research
bio-methylation-methylkit
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.
2.85k repo starsObserved in 10 repos
Research
bio-pathway-gsea
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arbitrary significance cutoffs. Detects subtle but coordinated expression changes.
2.85k repo starsObserved in 10 repos
Research
genome-compare
Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
2.85k repo starsObserved in 10 repos
Research
bio-alignment-msa-statistics
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
2.85k repo starsObserved in 9 repos
Research
claw-ancestry-pca
Ancestry decomposition PCA against the Simons Genome Diversity Project
2.85k repo starsObserved in 9 repos
Research
foldseek
Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.
2.85k repo starsObserved in 9 repos
Research