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scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

77K 2K 447
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
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.

62K 68 10
scverse
squidpy

Spatial Single Cell Analysis in Python

43K 567 114
theislab
cellrank

CellRank: dynamics from multi-view single-cell data

9K 443 57
scverse
snapatac2

Single-cell epigenomics analysis tools

7K 316 39
dpeerlab
palantir

Single cell trajectory detection

6K 309 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 447
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.

2K 115 15
yizhak-lab-ccg
scxpand

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

2K 8 4
yizhak-lab-ccg
scxpand-cuda

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

1K 8 4
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

1K 6 2
theislab
scgen

Single cell perturbation prediction

866 342 69
LiQian-XC
sctour

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

607 80 4
HelloWorldLTY
awgan

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

592 8 0
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.

583 18 3
Hon-lab
pyspade

Single cell Perturbations - Analysis of Differential gene Expression

287 8 0
calico
scnym

Semi supervised adversarial network networks for single cell classification

246 78 13
broadinstitute
single-cell-portal

Convenience scripts for Single Cell Portal

216 51 25
ddiez
singlecellhaystack

A Python implementation of singleCellHaystack.

209 13 1
GuangyuWangLab2021
celldancer

Predict RNA velocity through deep learning

201 73 12
jsxlei
scale-v2

Single-cell integrative Analysis via Latent feature Extraction

197 83 17
willjgh
interaction-inference

Inference of interaction between genes using constrained optimization

81 0 0
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