dburkhardt

patient-matching-of-clinical-trials-using-generative-ai

single-cell-best-practices

https://www.sc-best-practices.org

cellxgene-census

CZ CELLxGENE Discover Census

funkyheatmap

Visualising data frames as funky heatmaps 📊

cytopath

Simulation based inference of differentiation trajectories from RNA velocity fields.

CellOracle

This is the alpha version of the CellOracle package

scprep

A collection of scripts and tools for loading, processing, and handling single cell data.

scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

quarto-web

Quarto website

open-problems-multimodal

1st place solution of Kaggle Open Problems - Multimodal Single-Cell Integration

MultiVelo

Multi-omic velocity inference

website

Website hosted at https://openproblems.bio

neurips_2022_saturn_notebooks

Notebooks for exploring data associated with the Open Problems competition on Kaggle, presented at NeurIPS 2022

LearnableScattering

Learnable Geometric Scattering Network

neurips2021_multimodal_viash

dask-saturn

Python library for interacting with Dask clusters in Saturn

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

aerpod-project

I wrote a python native Kubernetes workflow orchestrator

FONtools

JSON-based FON (Feature Object Notation) format and tools to simplify genomic annotations usage

cellxgene

An interactive explorer for single-cell transcriptomics data

viash

script + metadata = standalone component

openproblems

Formalizing and benchmarking open problems in single-cell genomics

geosketch

Geometry-preserving random sampling

math-with-slack

Rendered math (MathJax) with Slack's desktop client

parler-grab

Archiving Parler.

PyTorch-VAE

A Collection of Variational Autoencoders (VAE) in PyTorch.

diffxpy

Differential expression analysis for single-cell RNA-seq data.

SingleCellWorkshop

UMAP-examples-mammoth-