Single Cell Genomics Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

tiledbsoma

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.

squidpy

Spatial Single Cell Analysis in Python

crested

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

cellrank

CellRank: dynamics from multi-view single-cell data

snapatac2

Single-cell epigenomics analysis tools

palantir

Single cell trajectory detection

scarches

Reference mapping for single-cell genomics

scvi

Deep probabilistic analysis of single-cell and spatial omics data

diffbio

End-to-end differentiable bioinformatics pipelines built on JAX/Flax NNX

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.

scxpand

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

scgen

Single cell perturbation prediction

scmalignantfinder

scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells from their normal counterparts.

scxpand-cuda

Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing (CUDA-enabled)

awgan

Codes for paper: AWGAN: A Powerful Batch Effect Removal Model for scRNA-seq Data

sctour

A deep learning architecture for robust inference and accurate prediction of cellular dynamics

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

tiledbsc

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.

celldancer

Study RNA velocity through neural network.

scnym

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

single-cell-portal

Convenience scripts for Single Cell Portal

pyspade

Single cell Perturbations - Analysis of Differential gene Expression

singlecellhaystack

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).