PyPI Stats
  • Insights
  • PyPI
  • GitHub
  • Search
  • Compare
  • Advisories
  • Ecosystem
  • About
Home

Scverse Python Packages

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

Annotated data.

2M 736 191
scverse
scanpy

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

822K 2K 741
scverse
mudata

Multimodal Data (.h5mu) implementation for Python

151K 120 22
scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

79K 2K 447
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.

60K 68 10
scverse
muon

muon is a multimodal omics Python framework

28K 266 36
scverse
pertpy

Single-cell perturbation analysis

7K 309 56
scverse
rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

7K 360 43
icbi-lab
infercnvpy

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

3K 189 32
theislab
ehrapy

Electronic Health Record Analysis with Python.

3K 347 45
YosefLab
scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 447
complextissue
pyclustree

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

2K 14 0
scverse
rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

2K 360 43
scverse
rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

2K 360 43
colganwi
treedata

anndata with trees

918 8 3
cantinilab
grnndata

Awesome GRN enhanced AnnData toolkit

835 11 2
complextissue
pytximport

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

737 44 2
complextissue
spatiomic

A Python package for unsupervised analysis of spatial (prote)omics data.

616 17 0
john-mulvey
pylimma

Python port of R limma for differential expression analysis

402 0 0
metaspace2020
metaspace-converter

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

324 16 1
MannLabs
alphapepttools

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

217 18 2
YosefLab
pycea-lineage

scverse lineage tracing analysis toolkit

156 4 2
gtca
chame

Chromatin analysis module

79 4 0
csglab
gedi2py

A high-performance Python package for single-cell genomics

69 1 0
    • Data from PyPI, GitHub, ClickHouse, and BigQuery