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seandavi/awesome-single-cell

A curated list of software packages and data resources for single-cell analysis, including RNA-seq and ATAC-seq.

3.7K

Active

Databases

CLI Tools

#bioinformatics#single-cell#rna-seq

scverse/scanpy

Single-cell analysis in Python, scaling to >100M cells.

2.4K

Active

Python

React

#single-cell analysis#bioinformatics#data-science

scverse/scvi-tools

A Python library for deep probabilistic analysis of single-cell and spatial omics data.

1.6K

Active

Python

Computer Vision

Databases

Python

#single-cell-genomics#variational-autoencoder#deep-learning

theislab/single-cell-tutorial

A tutorial for best practices in single-cell RNA-seq analysis, useful for bioinformatics developers.

1.6K

Archived

Jupyter Notebook

Tutorials & Courses

ORMs & Query Builders

#bioinformatics#single-cell-analysis#rna-seq

bowang-lab/scGPT

A GitHub repository for scGPT, a single-cell GPT model, with Jupyter Notebook and foundation-model related topics.

1.5K

Stable

Jupyter Notebook

#single-cell-gpt#foundation-model#gpt

theislab/single-cell-best-practices

A comprehensive guide for best practices in single-cell RNA sequencing analysis.

1.2K

Active

Jupyter Notebook

Tutorials & Courses

Databases

#rna-seq#single-cell#tutorial

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