timtreis

scikit-learn

scikit-learn: machine learning in Python

shap

A game theoretic approach to explain the output of any machine learning model.

Startup-CTO-Handbook

The Startup CTO's Handbook, a book covering leadership, management and technical topics for leaders of software engineering teams

docopt

Create *beautiful* command-line interfaces with Python

github-changelog-generator

Automatically generate change log from your tags, issues, labels and pull requests on GitHub.

datashader

Quickly and accurately render even the largest data.

submitit

Python 3.8+ toolbox for submitting jobs to Slurm

single-cell-best-practices

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

GSEApy

Gene Set Enrichment Analysis in Python

squidpy

Spatial Single Cell Analysis in Python

ehrapy

Electronic Health Record Analysis with Python.

awesome-drug-discovery-knowledge-graphs

A collection of research papers, datasets and software related to knowledge graphs for drug discovery. Accompanies the paper "A review of biomedical datasets relating to drug discovery: a knowledge graph perspective" (Briefings in Bioinformatics, 2022)

Stereopy

A toolkit of spatial transcriptomic analysis.

pertpy

Perturbation Analysis in the scverse ecosystem.

pypath

Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

huggingmolecules

pycytominer

Python package for processing image-based profiling data

spatialdata-plot

Static plotting for spatialdata

paste2

Probabilistic Alignment of Spatial Transcriptomics Experiments v.2

Spaco

Spatially constrained color profiling for visualizing single-cell resolution spatial data

JUMP-Target

Lists and 384-well plate maps of compounds and genetic perturbations designed to assess connectivity in profiling assays

spatialdata_xenium_explorer

Interoperability between SpatialData and the Xenium Explorer

bionty

Registries for biological entities, coupled to public ontologies.

shadows

Shadow objects for AnnData and MuData (experimental)

DINO4Cells_code

This repo will contain the code for training DINO models and extracting features

gliberal-scMultipleX

Feature extraction and linking of multiplexing data.

jump-cpg0016-segmentation

Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium

SVGbench

Evaluating spatially variable gene detection methods for spatial transcriptomics data

sc_analysis_template

Template repository for analysis of single-cell data and tools.