Numerical differential equation solvers in JAX. Autodifferentiable and GPU-capable. https://docs.kidger.site/diffrax/

TISSUE (Transcript Imputation with Spatial Single-cell Uncertainty Estimation) provides tools for estimating well-calibrated uncertainty measures for gene expression predictions in single-cell spat…

Jupyter notebooks and scripts for generating data and figures associated with the TISSUE manuscript

A benchmark for few-shot evaluation of foundation models for electronic health records (EHRs)

FEMR (Framework for Electronic Medical Records) provides tooling for large-scale, self-supervised learning using electronic health records

Flax is a neural network library for JAX that is designed for flexibility.

Python SDK to interact with Cirro

Multi-omic single-cell optimal transport tools

Break the linear presentation of Jupyter Notebooks with sticky cells!

Solve ODEs fast, with support for PyMC

Aesara is a Python library for defining, optimizing, and efficiently evaluating mathematical expressions involving multi-dimensional arrays.

Sparse matrix tools extending scipy.sparse, but with incompatible licenses

A newer and more modern column tool.

Python package to read and write R RData and Rds files into/from pandas dataframes. No R or other external dependencies required.

Distributed Xarray with Apache Beam

Sparse multi-dimensional arrays for the PyData ecosystem

N-D labeled arrays and datasets in Python

Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective.

Formalizing and benchmarking open problems in single-cell genomics

Uniform Manifold Approximation and Projection

Tools to allow the reconstruction of tumor cell specific gene expression patterns from bulk RNA-seq samples

SciWiki: Collective KnowledgeBase for Scientific Data and Use

An intuitive library to add plotting functionality to scikit-learn objects.

Universal Analysis Pipeline - A python tool for controlled and coordinated data analysis

NumPy aware dynamic Python compiler using LLVM

Run ruff, isort, pyupgrade, mypy, pylint, flake8, and more on Jupyter Notebooks

Universal Analysis Pipeline - A python tool for controlled and coordinated data analysis

☄🌌️ The minimal, blazing-fast, and infinitely customizable prompt for any shell!

Python toolbox for optimization on Riemannian manifolds with support for automatic differentiation

A small utility to quickly tag studies and samples from the NCBI Gene Expression Omnibus (GEO) with a curses interface.