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Scverse Python Packages

Python packages with the GitHub topic scverse. Sorted by relevance, with stars and monthly downloads.
scverse
anndata

Annotated data.

1.7M 740 191
scverse
scanpy

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

828K 2K 742
scverse
mudata

Multimodal Data (.h5mu) implementation for Python

158K 121 22
scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

95K 2K 450
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
scverse
muon

muon is a multimodal omics Python framework

29K 267 35
scverse
pertpy

Single-cell perturbation analysis

6K 311 59
scverse
rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

5K 370 46
icbi-lab
infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

4K 189 32
theislab
ehrapy

Electronic Health Record Analysis with Python.

2K 350 45
scverse
rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

2K 370 46
YosefLab
scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 450
complextissue
pyclustree

A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.

2K 15 0
scverse
rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

2K 370 46
colganwi
treedata

anndata with trees

938 8 3
cantinilab
grnndata

Awesome GRN enhanced AnnData toolkit

638 11 2
complextissue
pytximport

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

595 45 2
john-mulvey
pylimma

Python port of R limma for differential expression analysis

478 1 0
complextissue
spatiomic

A python toolbox for spatial omics analysis.

412 17 0
MannLabs
alphapepttools

Search- and quantification-engine agnostic biological interpretation of proteomics data

310 19 2
metaspace2020
metaspace-converter

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

263 16 1
YosefLab
pycea-lineage

Scverse lineage tracing toolkit

143 4 2
gtca
chame

Chromatin analysis module

90 4 0
csglab
gedi2py

A high-performance Python package for single-cell genomics

70 2 0
    • Data from PyPI, GitHub, ClickHouse, and BigQuery