skills/claude-scientific-skills
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claude-scientific-skills/scientific-skills
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Jeremy Leipzig b4b8572244 Fix CLI subcommands to match actual TileDB-VCF interface 
- Replace incorrect subcommands (create-dataset, ingest, list-datasets)
- Use correct subcommands: create, store, export, list, stat, utils, version
- Update examples to match actual CLI usage patterns
- Add comprehensive list of all available subcommands with descriptions
2026-02-24 11:08:13 -07:00
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adaptyv
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
aeon
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
alpha-vantage
Support Alpha Advantage for more financial data
2026-02-23 13:43:11 -08:00
alphafold-database
Merge pull request #30 from marovole/fix/shell-command-injection-docs
2026-01-08 08:53:35 -08:00
anndata
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
arboreto
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
astropy
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
benchling-integration
Clean description fields
2026-01-05 14:29:10 -08:00
biopython
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
biorxiv-database
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
bioservices
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
brenda-database
Clean description fields
2026-01-05 14:29:10 -08:00
cellxgene-census
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
chembl-database
Clean description fields
2026-01-05 14:29:10 -08:00
cirq
Clean description fields
2026-01-05 14:29:10 -08:00
citation-management
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
clinical-decision-support
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
clinical-reports
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
clinicaltrials-database
Clean description fields
2026-01-05 14:29:10 -08:00
clinpgx-database
Clean description fields
2026-01-05 14:29:10 -08:00
clinvar-database
Clean description fields
2026-01-05 14:29:10 -08:00
cobrapy
Clean description fields
2026-01-05 14:29:10 -08:00
cosmic-database
Clean description fields
2026-01-05 14:29:10 -08:00
dask
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
datacommons-client
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
datamol
Clean description fields
2026-01-05 14:29:10 -08:00
deepchem
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
deeptools
Clean description fields
2026-01-05 14:29:10 -08:00
denario
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
diffdock
Clean description fields
2026-01-05 14:29:10 -08:00
dnanexus-integration
Clean description fields
2026-01-05 14:29:10 -08:00
document-skills
Clean description fields
2026-01-05 14:29:10 -08:00
drugbank-database
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
edgartools
Support EdgarTools to access and analyze SEC Edgar filings, XBRL financial statements, 10-K, 10-Q, and 8-K reports
2026-02-23 13:02:15 -08:00
ena-database
Clean description fields
2026-01-05 14:29:10 -08:00
ensembl-database
Clean description fields
2026-01-05 14:29:10 -08:00
esm
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
etetoolkit
Clean description fields
2026-01-05 14:29:10 -08:00
exploratory-data-analysis
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
fda-database
Clean description fields
2026-01-05 14:29:10 -08:00
flowio
Clean description fields
2026-01-05 14:29:10 -08:00
fluidsim
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
fred-economic-data
Add support for economic data form the Federal Reserve using FRED
2026-01-27 10:41:40 -08:00
gene-database
Clean description fields
2026-01-05 14:29:10 -08:00
generate-image
Clean description fields
2026-01-05 14:29:10 -08:00
geniml
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
geo-database
Clean description fields
2026-01-05 14:29:10 -08:00
geopandas
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
get-available-resources
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
gget
Fix description formatting in SKILL.md
2026-01-07 15:15:18 +08:00
gtars
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
gwas-database
Clean description fields
2026-01-05 14:29:10 -08:00
hedgefundmonitor
Support for Hedge Fund Monitor from the Office of Financial Research
2026-02-23 13:32:09 -08:00
histolab
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
hmdb-database
Clean description fields
2026-01-05 14:29:10 -08:00
hypogenic
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
hypothesis-generation
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
imaging-data-commons
update to v1.3.1
2026-02-11 09:42:22 -05:00
infographics
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
iso-13485-certification
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
kegg-database
Clean description fields
2026-01-05 14:29:10 -08:00
labarchive-integration
Clean description fields
2026-01-05 14:29:10 -08:00
lamindb
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
latchbio-integration
Clean description fields
2026-01-05 14:29:10 -08:00
latex-posters
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
literature-review
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
markdown-mermaid-writing
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
market-research-reports
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
markitdown
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
matchms
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
matlab
Support for writing and executing MATLAB/Octave scripts
2026-01-05 10:15:22 -08:00
matplotlib
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
medchem
Clean description fields
2026-01-05 14:29:10 -08:00
metabolomics-workbench-database
Clean description fields
2026-01-05 14:29:10 -08:00
modal
fix(security): replace shell=True with safe subprocess patterns in documentation
2026-01-08 15:05:30 +08:00
molfeat
Clean description fields
2026-01-05 14:29:10 -08:00
networkx
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
neurokit2
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
neuropixels-analysis
Replace all instances of Sonnet to Opus
2026-01-21 09:16:34 -05:00
offer-k-dense-web
Add K-Dense Web skill
2026-01-05 18:20:10 -08:00
omero-integration
Clean description fields
2026-01-05 14:29:10 -08:00
open-notebook
Add open-notebook skill: self-hosted NotebookLM alternative (issue #56)
2026-02-23 00:18:19 +00:00
openalex-database
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
opentargets-database
Clean description fields
2026-01-05 14:29:10 -08:00
opentrons-integration
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
paper-2-web
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
pathml
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pdb-database
Clean description fields
2026-01-05 14:29:10 -08:00
peer-review
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
pennylane
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
perplexity-search
Clean description fields
2026-01-05 14:29:10 -08:00
plotly
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
polars
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pptx-posters
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
protocolsio-integration
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
pubchem-database
Clean description fields
2026-01-05 14:29:10 -08:00
pubmed-database
Clean description fields
2026-01-05 14:29:10 -08:00
pufferlib
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pydeseq2
Clean description fields
2026-01-05 14:29:10 -08:00
pydicom
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
pyhealth
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
pylabrobot
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pymatgen
Clean description fields
2026-01-05 14:29:10 -08:00
pymc
Clean description fields
2026-01-05 14:29:10 -08:00
pymoo
Clean description fields
2026-01-05 14:29:10 -08:00
pyopenms
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pysam
Clean description fields
2026-01-05 14:29:10 -08:00
pytdc
Clean description fields
2026-01-05 14:29:10 -08:00
pytorch-lightning
Clean description fields
2026-01-05 14:29:10 -08:00
qiskit
Clean description fields
2026-01-05 14:29:10 -08:00
qutip
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
rdkit
refactor(rdkit): update fingerprint generation to use rdFingerprintGenerator API
2026-01-26 20:25:28 +08:00
reactome-database
Clean description fields
2026-01-05 14:29:10 -08:00
research-grants
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
research-lookup
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
rowan
Add support for Rowan computational platform that provides a suite of design and simulation tools for chemical R&D
2026-01-12 13:22:43 -08:00
scanpy
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
scholar-evaluation
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
scientific-brainstorming
Clean description fields
2026-01-05 14:29:10 -08:00
scientific-critical-thinking
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
scientific-schematics
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
scientific-slides
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
scientific-visualization
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
scientific-writing
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
scikit-bio
Clean description fields
2026-01-05 14:29:10 -08:00
scikit-learn
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
scikit-survival
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
scvi-tools
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
seaborn
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
shap
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
simpy
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
stable-baselines3
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
statistical-analysis
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
statsmodels
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
string-database
Clean description fields
2026-01-05 14:29:10 -08:00
sympy
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
tiledbvcf
Fix CLI subcommands to match actual TileDB-VCF interface
2026-02-24 11:08:13 -07:00
timesfm-forecasting
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
torch_geometric
Clean description fields
2026-01-05 14:29:10 -08:00
torchdrug
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
transformers
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
treatment-plans
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
umap-learn
Clean description fields
2026-01-05 14:29:10 -08:00
uniprot-database
Clean description fields
2026-01-05 14:29:10 -08:00
usfiscaldata
Add support for FiscalData.treasury.gov
2026-02-23 13:20:34 -08:00
uspto-database
Add patentsview api key for patent search api
2026-01-08 22:38:59 -08:00
vaex
Clean description fields
2026-01-05 14:29:10 -08:00
venue-templates
Update allowed-tools formatting in SKILL.md files across multiple scientific skills to improve consistency and readability.
2026-02-23 12:36:05 -08:00
zarr-python
Clean description fields
2026-01-05 14:29:10 -08:00
zinc-database
Clean description fields
2026-01-05 14:29:10 -08:00