skills/claude-scientific-skills
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claude-scientific-skills/scientific-skills
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Andrey Fedorov 0c4a7eaf16 Update imaging-data-commons skill to v1.4.0 
Release notes:
- Bump idc-index requirement to 0.11.10
- digital_pathology_guide.md: add "Filter by specimen preparation" section
  with H&E staining and FFPE/frozen embedding query examples (array column syntax)
- digital_pathology_guide.md: add "Identifying Tumor vs Normal Slides" section
  covering primaryAnatomicStructureModifier_CodeMeaning (all SM collections)
  and TCGA barcode parsing via ContainerIdentifier (TCGA-specific)
- digital_pathology_guide.md: add "Finding Pre-Computed Analysis Results" section
  for discovering derived datasets (nuclei segmentations, TIL maps) via
  analysis_results_index
- digital_pathology_guide.md: document per-annotation measurements in DICOM ANN
  objects (extraction via highdicom post-download, link to tutorial notebook)
- digital_pathology_guide.md: update sm_index description with new columns
  (container/slide ID, tissue type, anatomic structure, diagnosis)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
2026-03-04 17:26:57 -05:00
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adaptyv
Cleanup
2026-03-03 08:20:03 -08:00
aeon
Cleanup
2026-03-03 08:20:03 -08:00
alpha-vantage
Support Alpha Advantage for more financial data
2026-02-23 13:43:11 -08:00
alphafold-database
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2026-03-03 08:20:03 -08:00
anndata
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arboreto
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astropy
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2026-03-03 08:20:03 -08:00
benchling-integration
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2026-03-03 08:20:03 -08:00
bgpt-paper-search
Add BGPT paper search skill
2026-02-24 14:42:31 -07:00
bindingdb-database
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
biopython
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biorxiv-database
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bioservices
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brenda-database
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2026-03-03 08:20:03 -08:00
cbioportal-database
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
cellxgene-census
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chembl-database
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cirq
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citation-management
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clinical-decision-support
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clinical-reports
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clinicaltrials-database
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clinpgx-database
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clinvar-database
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cobrapy
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2026-03-03 08:20:03 -08:00
consciousness-council
feat: add cognitive science skills — consciousness-council, dhdna-profiler, what-if-oracle
2026-03-02 17:16:09 +02:00
cosmic-database
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dask
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datacommons-client
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datamol
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deepchem
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deeptools
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denario
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2026-03-03 08:20:03 -08:00
depmap
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
dhdna-profiler
feat: add cognitive science skills — consciousness-council, dhdna-profiler, what-if-oracle
2026-03-02 17:16:09 +02:00
diffdock
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2026-03-03 08:20:03 -08:00
dnanexus-integration
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document-skills
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drugbank-database
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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
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ensembl-database
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esm
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etetoolkit
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exploratory-data-analysis
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fda-database
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flowio
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fluidsim
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fred-economic-data
Add support for economic data form the Federal Reserve using FRED
2026-01-27 10:41:40 -08:00
gene-database
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generate-image
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geniml
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geo-database
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geomaster
Add GeoMaster: Comprehensive Geospatial Science Skill
2026-03-01 13:42:41 +05:00
geopandas
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get-available-resources
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gget
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2026-03-03 08:20:03 -08:00
ginkgo-cloud-lab
Support for Ginkgo Cloud Lab
2026-03-02 09:53:41 -08:00
glycoengineering
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
gnomad-database
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
gtars
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2026-03-03 08:20:03 -08:00
gtex-database
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
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gwas-database
Cleanup
2026-03-03 08:20:03 -08:00
hedgefundmonitor
Support for Hedge Fund Monitor from the Office of Financial Research
2026-02-23 13:32:09 -08:00
histolab
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hmdb-database
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hypogenic
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hypothesis-generation
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2026-03-03 08:20:03 -08:00
imaging-data-commons
Update imaging-data-commons skill to v1.4.0
2026-03-04 17:26:57 -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
interpro-database
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
iso-13485-certification
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2026-03-03 08:20:03 -08:00
jaspar-database
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
kegg-database
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2026-03-03 08:20:03 -08:00
labarchive-integration
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lamindb
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latchbio-integration
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2026-03-03 08:20:03 -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
Cleanup
2026-03-03 08:20:03 -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
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2026-03-03 08:20:03 -08:00
markitdown
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matchms
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matlab
Support for writing and executing MATLAB/Octave scripts
2026-01-05 10:15:22 -08:00
matplotlib
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medchem
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metabolomics-workbench-database
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modal
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molecular-dynamics
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
molfeat
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2026-03-03 08:20:03 -08:00
monarch-database
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
networkx
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neurokit2
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neuropixels-analysis
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2026-03-03 08:20:03 -08:00
offer-k-dense-web
Add K-Dense Web skill
2026-01-05 18:20:10 -08:00
omero-integration
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2026-03-03 08:20:03 -08:00
open-notebook
Fix architecture diagram in markdown
2026-02-23 22:52:10 -05:00
openalex-database
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opentargets-database
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opentrons-integration
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paper-2-web
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parallel-web
Added parallel-web skill
2026-03-01 07:36:19 -08:00
pathml
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pdb-database
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peer-review
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pennylane
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perplexity-search
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2026-03-03 08:20:03 -08:00
phylogenetics
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
plotly
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polars
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pptx-posters
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protocolsio-integration
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pubchem-database
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pubmed-database
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pufferlib
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pydeseq2
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pydicom
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pyhealth
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pylabrobot
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pymatgen
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pymc
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pymoo
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pyopenms
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pysam
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pytdc
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pytorch-lightning
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2026-03-03 08:20:03 -08:00
pyzotero
Update README and documentation to reflect the addition of the pyzotero skill and increment skill count from 147 to 148. Bump version to 2.24.0 in marketplace.json.
2026-02-27 09:38:51 -08:00
qiskit
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qutip
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rdkit
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reactome-database
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research-grants
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2026-03-03 08:20:03 -08:00
research-lookup
Added parallel-web skill
2026-03-01 07:36:19 -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
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scholar-evaluation
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scientific-brainstorming
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scientific-critical-thinking
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scientific-schematics
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scientific-slides
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scientific-visualization
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scientific-writing
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scikit-bio
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scikit-learn
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scikit-survival
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scvelo
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
2026-03-03 07:15:36 -05:00
scvi-tools
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seaborn
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shap
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simpy
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stable-baselines3
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statistical-analysis
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statsmodels
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string-database
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sympy
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2026-03-03 08:20:03 -08:00
tiledbvcf
Remove all reference documentation files and clean up references
2026-02-24 11:30:31 -07:00
timesfm-forecasting
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torch_geometric
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torchdrug
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transformers
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treatment-plans
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umap-learn
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uniprot-database
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2026-03-03 08:20:03 -08:00
usfiscaldata
Add support for FiscalData.treasury.gov
2026-02-23 13:20:34 -08:00
uspto-database
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2026-03-03 08:20:03 -08:00
vaex
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2026-03-03 08:20:03 -08:00
venue-templates
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2026-03-03 08:20:03 -08:00
what-if-oracle
feat: add cognitive science skills — consciousness-council, dhdna-profiler, what-if-oracle
2026-03-02 17:16:09 +02:00
zarr-python
Cleanup
2026-03-03 08:20:03 -08:00
zinc-database
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