dawe

turicreate

Turi Create simplifies the development of custom machine learning models.

cudf

cuDF - GPU DataFrame Library

datasharing

The Leek group guide to data sharing

coremltools

Core ML tools contain supporting tools for Core ML model conversion, editing, and validation.

tensorflow_macos

TensorFlow for macOS 11.0+ accelerated using Apple's ML Compute framework.

hdbscan

A high performance implementation of HDBSCAN clustering.

bolt

10x faster matrix and vector operations

POT

POT : Python Optimal Transport

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

seq

A high-performance, Pythonic language for bioinformatics

anndata

Annotated data.

nimfa

Nimfa: Nonnegative matrix factorization in Python

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

squidpy

Spatial Single Cell Analysis in Python

scvelo

RNA Velocity generalized through dynamical modeling

scarches

Reference mapping for single-cell genomics

openproblems

Formalizing and benchmarking open problems in single-cell genomics

muon

muon is a multimodal omics Python framework

GMatch4py

A graph matching library for Python

diffxpy

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

chromap

Fast alignment and preprocessing of chromatin profiles

netrd

A library for network {reconstruction, distances, dynamics}

scikit-fusion

scikit-fusion: Data fusion via collective latent factor models

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

REGAL

Representation learning-based graph alignment based on implicit matrix factorization and structural embeddings

mofax

Work with trained factor models in Python

batchglm

Fit generalized linear models in python.

PySeq2500

Control an Illumina HiSeq 2500 System

tagdust

A tool to extract mappable reads from various library preparation protocols.

SCRNA