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scverse
anndata

Annotated data.

2.1M 736 191
scverse
scanpy

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

815K 2K 741
scverse
mudata

Multimodal Data (.h5mu) implementation for Python

147K 120 22
srivarra
annsel

A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.

39K 17 2
scverse
muon

muon is a multimodal omics Python framework

28K 266 36
scverse
rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

7K 360 43
lilab-bcb
cirrocumulus

Bring your single-cell data to life

4K 97 18
noamteyssier
adpbulk

pseudobulking on an AnnData object

4K 35 1
yizhak-lab-ccg
scxpand

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

2K 8 4
scverse
rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

2K 360 43
NygenAnalytics
cytetype

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

2K 127 17
ArpiarSaundersLab
annsql

The AnnSQL package enables SQL based queries on AnnData objects.

2K 41 2
scverse
rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

1K 360 43
yizhak-lab-ccg
scxpand-cuda

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

1K 8 4
theislab
drvi-py

Unsupervised Deep Disentangled Representation of Single-Cell Omics

1K 65 5
mvinyard
torch-adata

torch-adata: bridging AnnData-based data models to torch.

1K 21 0
colganwi
treedata

anndata with trees

854 8 3
cantinilab
grnndata

Awesome GRN enhanced AnnData toolkit

819 11 2
mvinyard
vintools

Michael Vinyard's utilities

772 2 2
theislab
geome

Geometric Learning for Genome Data

715 15 4
complextissue
pytximport

Feature-rich Python implementation of the tximport package for gene count estimation.

660 44 2
john-mulvey
pylimma

Python port of R limma for differential expression analysis

372 0 0
metaspace2020
metaspace-converter

Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

310 16 1
PMBio
mudatasets

Multimodal datasets, in MuData format

288 4 1
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