skills/claude-scientific-skills
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claude-scientific-skills/scientific-skills
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Robert 1e00b1536e Fix SpikeInterface API compatibility in neuropixels_pipeline.py 
- Change stream_name to stream_id in read_spikeglx() call
- Change output_folder to folder in run_sorter() call

These parameters were renamed in SpikeInterface ≥0.100.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-17 11:13:09 -05:00
..
adaptyv
Add support for Adaptyv for protein design
2025-11-24 19:52:45 -05:00
aeon
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
alphafold-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
anndata
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
arboreto
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
astropy
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
benchling-integration
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
biomni
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
biopython
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
biorxiv-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
bioservices
updated CHEMBL function calls
2025-11-21 12:52:30 +03:00
brenda-database
Add BRENDA database skill for enzyme research and analysis
2025-12-03 12:36:49 +08:00
cellxgene-census
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
chembl-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
cirq
Add support for Cirq: library for writing, manipulating, and optimizing quantum circuits, and then running them on quantum computers and quantum simulators.
2025-11-30 08:02:58 -05:00
citation-management
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
clinical-decision-support
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
clinical-reports
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
clinicaltrials-database
Consolidate skills
2025-11-13 18:50:42 -08:00
clinpgx-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
clinvar-database
Consolidate skills
2025-11-13 18:50:42 -08:00
cobrapy
Consolidate skills
2025-11-13 18:50:42 -08:00
cosmic-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
dask
Consolidate skills
2025-11-13 18:50:42 -08:00
datacommons-client
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
datamol
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
deepchem
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
deeptools
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
denario
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
diffdock
Consolidate skills
2025-11-13 18:50:42 -08:00
dnanexus-integration
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
document-skills
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
drugbank-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
ena-database
Consolidate skills
2025-11-13 18:50:42 -08:00
ensembl-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
esm
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
etetoolkit
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
exploratory-data-analysis
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
fda-database
Consolidate skills
2025-11-13 18:50:42 -08:00
flowio
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
fluidsim
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
gene-database
Consolidate skills
2025-11-13 18:50:42 -08:00
generate-image
Update all the latest writing skills
2025-12-12 11:42:41 -08:00
geniml
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
geo-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
geopandas
Add support for GeoPandas
2025-11-27 18:57:26 -05:00
get-available-resources
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
gget
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
gtars
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
gwas-database
Consolidate skills
2025-11-13 18:50:42 -08:00
histolab
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
hmdb-database
Consolidate skills
2025-11-13 18:50:42 -08:00
hypogenic
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
hypothesis-generation
Update all the latest writing skills
2025-12-12 11:42:41 -08:00
kegg-database
Consolidate skills
2025-11-13 18:50:42 -08:00
labarchive-integration
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
lamindb
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
latchbio-integration
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
latex-posters
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
literature-review
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
market-research-reports
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
markitdown
Update all the latest writing skills
2025-12-12 11:42:41 -08:00
matchms
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
matplotlib
Consolidate skills
2025-11-13 18:50:42 -08:00
medchem
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
metabolomics-workbench-database
Consolidate skills
2025-11-13 18:50:42 -08:00
modal
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
molfeat
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
networkx
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
neurokit2
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
neuropixels-analysis
Fix SpikeInterface API compatibility in neuropixels_pipeline.py
2025-12-17 11:13:09 -05:00
omero-integration
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
openalex-database
Add support for OpenAlex
2025-11-19 13:38:32 -08:00
opentargets-database
Consolidate skills
2025-11-13 18:50:42 -08:00
opentrons-integration
Consolidate skills
2025-11-13 18:50:42 -08:00
paper-2-web
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
pathml
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pdb-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
peer-review
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
pennylane
Add support for PennyLane: a cross-platform library for quantum computing, quantum machine learning, and quantum chemistry.
2025-11-30 08:27:24 -05:00
perplexity-search
Add Perplexity search
2025-11-16 16:16:21 -08:00
plotly
Add Plotly support
2025-11-27 18:47:08 -05:00
polars
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pptx-posters
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
protocolsio-integration
Consolidate skills
2025-11-13 18:50:42 -08:00
pubchem-database
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pubmed-database
Consolidate skills
2025-11-13 18:50:42 -08:00
pufferlib
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pydeseq2
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pydicom
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pyhealth
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pylabrobot
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pymatgen
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pymc
Consolidate skills
2025-11-13 18:50:42 -08:00
pymoo
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pyopenms
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pysam
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pytdc
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
pytorch-lightning
Consolidate skills
2025-11-13 18:50:42 -08:00
qiskit
Add support for Qiskit from IBM: software stack for quantum computing and algorithms research. Build, optimize, and execute quantum workloads at scale.
2025-11-30 08:46:41 -05:00
qutip
Add support for QuTiP: an open-source software for simulating the dynamics of open quantum systems.
2025-11-30 07:46:17 -05:00
rdkit
Consolidate skills
2025-11-13 18:50:42 -08:00
reactome-database
Fix Reactome database nesting
2025-11-30 06:28:41 -05:00
research-grants
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
research-lookup
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
scanpy
Consolidate skills
2025-11-13 18:50:42 -08:00
scholar-evaluation
Update all the latest writing skills
2025-12-12 11:42:41 -08:00
scientific-brainstorming
Consolidate skills
2025-11-13 18:50:42 -08:00
scientific-critical-thinking
Update all the latest writing skills
2025-12-12 11:42:41 -08:00
scientific-schematics
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
scientific-slides
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
scientific-visualization
Consolidate skills
2025-11-13 18:50:42 -08:00
scientific-writing
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
scikit-bio
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
scikit-learn
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
scikit-survival
Consolidate skills
2025-11-13 18:50:42 -08:00
scvi-tools
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
seaborn
Consolidate skills
2025-11-13 18:50:42 -08:00
shap
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
simpy
Consolidate skills
2025-11-13 18:50:42 -08:00
stable-baselines3
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
statistical-analysis
Consolidate skills
2025-11-13 18:50:42 -08:00
statsmodels
Consolidate skills
2025-11-13 18:50:42 -08:00
string-database
Consolidate skills
2025-11-13 18:50:42 -08:00
sympy
Consolidate skills
2025-11-13 18:50:42 -08:00
torch_geometric
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
torchdrug
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
transformers
Consolidate skills
2025-11-13 18:50:42 -08:00
treatment-plans
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
umap-learn
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
uniprot-database
refactor: replace manual argv parsing with argparse
2025-11-29 01:13:05 -05:00
uspto-database
refactor: replace manual argv parsing with argparse
2025-11-29 01:13:05 -05:00
vaex
Consolidate skills
2025-11-13 18:50:42 -08:00
venue-templates
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
zarr-python
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
zinc-database
Consolidate skills
2025-11-13 18:50:42 -08:00