Skill collection
jaechang-hits/SciAgent-Skills agent skills
- skills
- 169
- GitHub stars
- 374
GitHub description: “197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.”
- Stars
- 374 (40 forks)
- Licence
- Unknown
- Last push
- Sep 2026
- Created
- Feb 2026
- Homepage
- omicshorizon.ai/en
- ai-agent
- bioinformatics
- claude-code
- claude-plugin
- drug-discovery
- genomics
- life-sciences
- scientific-computing
- claude-skills
- open-source
- proteomics
- scientific-skills
- biostatistics
- cheminformatics
- computational-biology
- rna-seq
Install all skills
npx skills add jaechang-hits/SciAgent-SkillsAdd --skill <name> for a single skill and -a <agent> to choose the agent (see the agent guides).
Skills in jaechang-hits/SciAgent-Skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. | jaechang-hits/ | 374 | — | ~4k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 2 | 3Dmol.js WebGL molecular visualization emitted as self-contained HTML. | jaechang-hits/ | 374 | — | ~3.2k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 3 | Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. | jaechang-hits/ | 374 | 1 repo | ~4.9k | Automated safety check: Pass | GPL-2.0 | 12 days ago |
| 4 | Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. | jaechang-hits/ | 374 | — | ~6.9k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 5 | Programmatic PubMed access via NCBI E-utilities REST API. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.4k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 6 | Scaffold a new SciAgent-Skills entry. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | — | ~2.3k | Automated safety check: Pass | Unknown | 12 days ago |
| 7 | Model interpretability via SHAP (Shapley values from game theory). | jaechang-hits/ | 374 | 1 repo | ~3.7k | Automated safety check: Pass | MIT | 12 days ago |
| 8 | Annotated matrices for single-cell genomics. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~5.8k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 9 | Methodology for exploratory data analysis on scientific files. | jaechang-hits/ | 374 | — | ~3.1k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 10 | 10.Scikit Bio Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination… | jaechang-hits/ | 374 | — | ~4.4k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 11 | Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes. | jaechang-hits/ | 374 | 1 repo | ~3.9k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 12 | Guidelines for clinical decision support (CDS) documents: biomarker-stratified cohort analyses and GRADE-graded treatment reports. | jaechang-hits/ | 374 | 1 repo | ~3k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 13 | Automated scRNA-seq cell type annotation via pre-trained logistic regression. | jaechang-hits/ | 374 | 2 repos | ~5.4k | Automated safety check: Pass | MIT | 12 days ago |
| 14 | ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. | jaechang-hits/ | 374 | 2 repos | ~8.5k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 15 | Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via… | jaechang-hits/ | 374 | 2 repos | ~6.9k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 16 | Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. | jaechang-hits/ | 374 | 2 repos | ~7.2k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 17 | 17.Geo Database NCBI GEO access via GEOparse and E-utilities. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~4.3k | Automated safety check: Pass | MIT | 12 days ago |
| 18 | Unified CLI/Python interface to 20+ genomic databases. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~5.3k | Automated safety check: Pass | BSD-2-Clause | 12 days ago |
| 19 | Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~4k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 20 | Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. | jaechang-hits/ | 374 | 2 repos | ~3.2k | Automated safety check: Pass | Unknown | 12 days ago |
| 21 | NCBI Gene via E-utilities: curated records across 1M+ taxa. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.4k | Automated safety check: Pass | CC0-1.0 | 12 days ago |
| 22 | Geospatial vector analysis extending pandas. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~3.8k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 23 | Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. | jaechang-hits/ | 374 | 1 repo | ~3.6k | Automated safety check: Pass | GPL-2.0 | 12 days ago |
| 24 | Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene). | jaechang-hits/ | 374 | 1 repo | ~4.7k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 25 | Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. | jaechang-hits/ | 374 | 1 repo | ~3.8k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 26 | Evaluating scientific evidence and claims. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.7k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 27 | Guide for annotating statistical significance (p-value asterisks) on comparison plots. | jaechang-hits/ | 374 | 1 repo | ~3k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 28 | Symbolic math in Python: exact algebra, calculus (derivatives, integrals, limits), equation solving, symbolic matrices, ODEs, code gen (lambdify, C/Fortran). | jaechang-hits/ | 374 | 1 repo | ~3.9k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 29 | Access AlphaFold DB's 200M+ predicted structures by UniProt ID. | jaechang-hits/ | 374 | 1 repo | ~4.1k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 30 | Molecular docking with AutoDock Vina (Python API). An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 31 | Molecular featurization hub (100+ featurizers) for ML. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.3k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 32 | Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. | jaechang-hits/ | 374 | 1 repo | ~4.5k | Automated safety check: Pass | MIT | 12 days ago |
| 33 | Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure… | jaechang-hits/ | 374 | 1 repo | ~4.5k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 34 | scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. | jaechang-hits/ | 374 | 1 repo | ~4.7k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 35 | Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. | jaechang-hits/ | 374 | 1 repo | ~4.8k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 36 | Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). | jaechang-hits/ | 374 | 1 repo | ~4.2k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 37 | GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). | jaechang-hits/ | 374 | 2 repos | ~5.3k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 38 | Infer and visualize intercellular communication from scRNA-seq with CellChat (R). | jaechang-hits/ | 374 | 2 repos | ~6.8k | Automated safety check: Pass | MIT | 12 days ago |
| 39 | Harmony batch correction for scRNA-seq and other omics. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~5.6k | Automated safety check: Pass | MIT | 12 days ago |
| 40 | Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~6.5k | Automated safety check: Pass | LGPL-3.0 | 12 days ago |
| 41 | Multi-modal single-cell analysis with muon/MuData. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~8.1k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 42 | Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with… | jaechang-hits/ | 374 | 2 repos | ~7.2k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 43 | Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. | jaechang-hits/ | 374 | 1 repo | ~6k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 44 | Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic… | jaechang-hits/ | 374 | 1 repo | ~8.5k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 45 | Cancer genomics (TCGA et al.) via cBioPortal REST API. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~8.2k | Automated safety check: Pass | AGPL-3.0 | 12 days ago |
| 46 | JASPAR 2024 TF binding profiles via REST API and pyJASPAR. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~7.1k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 47 | Build, read, validate, modify SBML biological network models via the libSBML Python API. | jaechang-hits/ | 374 | 1 repo | ~8.8k | Automated safety check: Pass | LGPL-2.1 | 12 days ago |
| 48 | Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. | jaechang-hits/ | 374 | 1 repo | ~6.6k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
Questions, answered from the data.
What is the best skill in jaechang-hits/SciAgent-Skills?
Neb Irc Activation Energy from jaechang-hits/SciAgent-Skills ranks first of the 169 skills in jaechang-hits/SciAgent-Skills listed here, with the highest score: its repository has 374 GitHub stars, its SKILL.md loads about 4k tokens and it passes the automated safety check with no findings. Next come Molecular Visualization 3dmol and Cobrapy Metabolic Modeling.
Are the skills in jaechang-hits/SciAgent-Skills official?
None yet. All 169 skills in jaechang-hits/SciAgent-Skills listed here come from community repositories; a skill counts as official when the product's own GitHub organization publishes it.
How do I install all skills from jaechang-hits/SciAgent-Skills?
Run npx skills add jaechang-hits/SciAgent-Skills in your project: the open-source skills CLI installs the repository's skills into your coding agent's skills folder. To install a single skill, open its page here for the exact command.
How are these skills ranked?
By Skill Navigator score, which combines the GitHub stars of the skill's repository (shared across that repo's skills and discounted for large collections), how many other GitHub owners carry a copy of the skill, and automated SKILL.md quality checks, minus penalties for safety-check warnings and for each further skill from the same repository. Skills that fail the safety check are not listed.