Robert
312f18ae60
Add neuropixels-analysis skill for extracellular electrophysiology
...
Adds comprehensive toolkit for analyzing Neuropixels high-density neural
recordings using SpikeInterface, Allen Institute, and IBL best practices.
Features:
- Data loading from SpikeGLX, Open Ephys, and NWB formats
- Preprocessing pipelines (filtering, phase shift, CAR, bad channel detection)
- Motion/drift estimation and correction
- Spike sorting integration (Kilosort4, SpykingCircus2, Mountainsort5)
- Quality metrics computation (SNR, ISI violations, presence ratio)
- Automated curation using Allen/IBL criteria
- AI-assisted visual curation for uncertain units
- Export to Phy and NWB formats
Supports Neuropixels 1.0 and 2.0 probes.
🤖 Generated with [Claude Code](https://claude.com/claude-code )
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com >
2025-12-17 11:06:28 -05:00
Timothy Kassis
78331e1b37
Remove all writing skills for upcoming upgrade
2025-12-07 13:54:58 -08:00
Timothy Kassis
ab4aff4670
Update README.md to include a promotional note for k-dense.ai, enhancing visibility of advanced capabilities.
2025-12-07 13:41:35 -08:00
Timothy Kassis
6560f1d779
Change Flux.2-dev to flex since dev does not exist
2025-12-04 14:50:30 -08:00
Timothy Kassis
49567890a6
Add BRENDA enzyme database
2025-12-03 17:29:05 -08:00
Timothy Kassis
90de96a99b
Add support for generating scientific illustrations using Nano Banan Pro and Flux.2 Pro
2025-11-30 09:30:58 -05:00
Timothy Kassis
7e8deebf96
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
Timothy Kassis
7763491813
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
Timothy Kassis
16e47a1755
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
Timothy Kassis
a077cee836
Add support for QuTiP: an open-source software for simulating the dynamics of open quantum systems.
2025-11-30 07:46:17 -05:00
Timothy Kassis
6ac2a15e39
Add support for GeoPandas
2025-11-27 18:57:26 -05:00
Timothy Kassis
41f272c2bd
Add Plotly support
2025-11-27 18:47:08 -05:00
Timothy Kassis
ea638c5618
Add support for Adaptyv for protein design
2025-11-24 19:52:45 -05:00
Timothy Kassis
65b39d45d6
Add support for OpenAlex
2025-11-19 13:38:32 -08:00
Timothy Kassis
c078c98ad2
Add Perplexity search
2025-11-16 16:16:21 -08:00
Timothy Kassis
2e80732340
Add uv installation instructions
2025-11-16 15:36:33 -08:00
Timothy Kassis
d94f21c51f
Add support for fluidsim for computational fluid dynamics
2025-11-13 19:46:29 -08:00
Timothy Kassis
54cab8e4b5
Update readme to clarify refactoring
2025-11-13 19:20:09 -08:00
Timothy Kassis
ad2dfc3446
Update readme
2025-11-13 19:17:42 -08:00
Timothy Kassis
cc99fdb57d
Add support for Modal so researchers can scale compute on demand for heavy computational tasks beyond running locally
2025-11-10 10:57:05 -08:00
Timothy Kassis
50fdaf1b04
Add Slack link
2025-11-10 09:24:36 -08:00
Timothy Kassis
0e4939147f
Link to examples
2025-11-06 17:05:17 -08:00
Timothy Kassis
1225ddecf1
Add support for both geniml and gtars
2025-11-04 10:22:03 -08:00
Timothy Kassis
63a4293f1a
Add support for the Denario AI scientist
2025-11-03 17:04:20 -08:00
Timothy Kassis
862445f531
Add support for Stable-Baselines3, a PyTorch-based library providing reliable, well-tested implementations of popular deep reinforcement learning algorithms with a simple and consistent API for research and training.
2025-11-02 14:54:16 -08:00
Timothy Kassis
b8c4d2bae1
Add support for PufferLib which is a high-performance, open-source Python toolkit that wraps complex RL environments to look like standard Gym/PettingZoo interfaces and supports massively parallel simulation (1M+ steps/sec) to accelerate deep reinforcement learning.
2025-11-02 14:52:06 -08:00
Timothy Kassis
27d6ee387f
Add support for Vaex for fast, memory-efficient exploration and visualization of large tabular datasets using lazy, out-of-core computation.
2025-11-02 14:43:20 -08:00
Timothy Kassis
f32b3f8b42
Add support for SymPY for symbolic mathematics that enables algebraic manipulation, equation solving, calculus, and symbolic computation directly in Python.
2025-11-02 14:30:20 -08:00
Timothy Kassis
ed2d1c4aeb
Add support for NetworkX for creating, analyzing, and visualizing complex networks and graphs.
2025-11-02 14:19:20 -08:00
Timothy Kassis
7e3fae3ad1
Add support to LaminDB
2025-10-31 11:39:54 -07:00
Timothy Kassis
97c03a11e5
Add Claude Code installation instructions
2025-10-31 11:21:01 -07:00
Timothy Kassis
b6bb261a71
Consolidate getting started
2025-10-31 09:49:48 -07:00
Haoxuan "Orion" Li
aa5018612f
Update README to include quick installation instructions for Cursor users and clarify MCP server usage across various clients.
2025-10-30 15:01:20 -07:00
Timothy Kassis
f12f9c2904
Enhance README by adding a call to action for users to star the repository, promoting visibility and ongoing maintenance.
2025-10-28 17:57:09 -07:00
Timothy Kassis
55af02f2d4
Add star history
2025-10-28 17:52:44 -07:00
Timothy Kassis
346010a1bf
Add Markitdown skill to read all sorts of documents
2025-10-28 16:31:01 -07:00
Timothy Kassis
5b37b62147
Update README to reflect the increase in equivalent tools from 500 to 1002
2025-10-28 15:54:00 -07:00
Timothy Kassis
82901e9fbe
Add hypothesis generation using HypoGeniC and HypoRefine
2025-10-28 12:53:43 -07:00
Timothy Kassis
981823a71a
Add ScholarEval as a thinking framework
2025-10-28 10:45:34 -07:00
Timothy Kassis
1f03feda5c
Add protocols.io integration
2025-10-26 11:09:03 -07:00
Timothy Kassis
44285238c4
Fix context initialization by using AGENTS.md instead of AGENT.md
2025-10-26 10:18:45 -07:00
Timothy Kassis
04d528c4bc
Added support for NeuroKit2
2025-10-25 21:38:31 -07:00
Timothy Kassis
a5c2ed9bb6
Add literature review skill
2025-10-25 10:55:36 -07:00
Timothy Kassis
295370a730
Update README.md to replace downloads and workflows badges with an equivalent tools badge for improved clarity.
2025-10-25 10:38:43 -07:00
Timothy Kassis
4fde8cb6de
Enhance README.md by adding a downloads badge to track total downloads of the project.
2025-10-24 19:41:22 -07:00
Timothy Kassis
564bd39835
Add support for HistoLab
2025-10-24 13:41:06 -07:00
Timothy Kassis
1871693348
Enhance README.md with detailed instructions for various workflows, emphasizing the importance of organized output and the creation of comprehensive documentation and visualizations.
2025-10-24 09:30:56 -07:00
Timothy Kassis
0e03bbcf38
Update readme
2025-10-24 09:23:19 -07:00
Timothy Kassis
ca6fd369d7
Add DrugBank access
2025-10-24 09:04:43 -07:00
Timothy Kassis
d923063309
Change license to MIT allowing commercial use!
2025-10-23 20:48:01 -07:00
