Single Cell Genomics Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

77K 2K 447

tiledbsoma

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

77K 124 30

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.

62K 68 10

squidpy

Spatial Single Cell Analysis in Python

43K 567 114

cellrank

CellRank: dynamics from multi-view single-cell data

9K 443 57

snapatac2

Single-cell epigenomics analysis tools

7K 316 39

palantir

Single cell trajectory detection

6K 309 61

scarches

Reference mapping for single-cell genomics

3K 404 70

scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 447

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.

2K 115 15

scxpand

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

2K 8 4

scxpand-cuda

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

1K 8 4

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

1K 6 2

scgen

Single cell perturbation prediction

866 342 69

sctour

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

607 80 4

awgan

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

592 8 0

scmalignantfinder

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

583 18 3