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Starred repositories
LLM agents for working with the SRA and associated bioinformatics databases.
Arc Virtual Cell Atlas
data-to-paper: Backward-traceable AI-driven scientific research
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
Install Jellyfin on your Samsung TV
ATAT is an email client for AI Agents. Deploy dozens of AI agents through a single email address (IMAP/SMTP) using the OpenAI API. Just add credentials, create one email and the aliases you need, a…
napari: a fast, interactive, multi-dimensional image viewer for python
Libraries and examples for programming your CleverPet Hub
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
An interactive explorer for single-cell transcriptomics data
An implementation of chunked, compressed, N-dimensional arrays for Python.
An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
This code package is for the Corrected-Fisher-Randomization (CFR) method. This method generates random surrogate data that preserves a specified set of first and second order marginal moments of a …
This code package is for the Tensor-Maximum-Entropy (TME) method. This method generates random surrogate data that preserves a specified set of first and second order marginal moments of a data ten…
build process for turning ipython notebooks into markdown files for your jekyll blog
Complete Matlab pipeline for large scale calcium imaging data analysis
Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.
2Photon Imaging and Electrophysiology Analysis code for the Datta Lab @ HMS
🏡 Open source home automation that puts local control and privacy first.