pavlin-policar

pytorch_geometric

Graph Neural Network Library for PyTorch

mlx

MLX: An array framework for Apple silicon

direnv

unclutter your .profile

fuzzywuzzy

Fuzzy String Matching in Python

wandb

🔥 A tool for visualizing and tracking your machine learning experiments. This repo contains the CLI and Python API.

BioGPT

typedb

TypeDB: the polymorphic database powered by types

pytorch_geometric_temporal

PyTorch Geometric Temporal: Spatiotemporal Signal Processing with Neural Machine Learning Models (CIKM 2021)

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

scispacy

A full spaCy pipeline and models for scientific/biomedical documents.

udocker

A basic user tool to execute simple docker containers in batch or interactive systems without root privileges.

bioicons

A library of free open source icons for science illustrations in biology and chemistry

keops

KErnel OPerationS, on CPUs and GPUs, with autodiff and without memory overflows

TDC

Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science

watermark

An IPython magic extension for printing date and time stamps, version numbers, and hardware information

python-ternary

:small_red_triangle: Ternary plotting library for python with matplotlib

jazzit

Laughs at your expense

daft

Render probabilistic graphical models using matplotlib

pybind11_examples

Examples for the usage of "pybind11"

leidenalg

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.

ivis

Dimensionality reduction in very large datasets using Siamese Networks

graphml-tutorials

Tutorials for Machine Learning on Graphs

PyNET-Bokeh

Rendering Realistic Bokeh Images with PyNET

PoincareMaps

The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

densvis

Density-preserving data visualization tools den-SNE and densMAP

umi-normalization

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

pybind_examples

Examples of pybind11 based projects (using cmake)

pvclust

boids

Simulated flocking of birds

procedural-landmass

Generate procedural landmass in Unity