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Single Cell Genomics Python Packages

Python packages with the GitHub topic single-cell-genomics. Sorted by relevance, with stars and monthly downloads.
scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

95K 2K 450
single-cell-data
tiledbsoma

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

77K 124 30
scverse
squidpy

Spatial Single Cell Analysis in Python

56K 569 113
aertslab
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.

41K 73 11
theislab
cellrank

CellRank: dynamics from multi-view single-cell data

10K 447 57
scverse
snapatac2

Single-cell epigenomics analysis tools

6K 319 40
dpeerlab
palantir

Single cell trajectory detection

6K 310 61
theislab
scarches

Reference mapping for single-cell genomics

3K 404 70
YosefLab
scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 450
avitai
diffbio

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

1K 1 0
parashardhapola
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.

1K 116 15
yizhak-lab-ccg
scxpand

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

1K 8 4
theislab
scgen

Single cell perturbation prediction

933 343 69
jonyyqn
scmalignantfinder

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

924 19 3
yizhak-lab-ccg
scxpand-cuda

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

803 8 4
HelloWorldLTY
awgan

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

755 8 0
LiQian-XC
sctour

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

649 81 4
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

648 6 2
single-cell-data
tiledbsc

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

303 125 30
GuangyuWangLab2021
celldancer

Study RNA velocity through neural network.

251 73 12
calico
scnym

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

201 78 13
broadinstitute
single-cell-portal

Convenience scripts for Single Cell Portal

200 51 25
Hon-lab
pyspade

Single cell Perturbations - Analysis of Differential gene Expression

189 8 0
ddiez
singlecellhaystack

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

183 13 1
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