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Scanpy Python Packages

Python packages with the GitHub topic scanpy. 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
muon

muon is a multimodal omics Python framework

28K 266 36
theislab
anndata2ri

Convert between AnnData and SingleCellExperiment

25K 149 19
lilab-bcb
cirrocumulus

Bring your single-cell data to life

4K 97 18
noamteyssier
adpbulk

pseudobulking on an AnnData object

4K 35 1
becavin-lab
checkatlas

One liner tool to check the quality of your single-cell atlases.

2K 3 2
cafferychen777
chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

2K 34 8
NygenAnalytics
cytetype

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

2K 127 17
FASTGenomics
fgread

Python readers for different data formats for FASTGenomics.

1K 1 1
colganwi
treedata

anndata with trees

918 8 3
cafferychen777
mllmcelltype

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

860 640 55
stefanpeidli
mousipy

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

714 30 5
prabhakarlab
pybanksy

BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.

578 78 15
cafferychen777
flashdeconv

Fast Linear Algebra for Scalable Hybrid Deconvolution of Spatial Transcriptomics

570 15 0
PMBio
mudatasets

Multimodal datasets, in MuData format

309 4 1
kenflab
llm-sc-curator

Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs.

300 3 0
theislab
ncem

Learning cell communication from spatial graphs of cells

268 117 13
cafferychen777
flashs

Flash-S: Frequency-domain Linearized Adaptive Spatial Hypothesis testing via Sketching

195 0 0
YosefLab
pycea-lineage

scverse lineage tracing analysis toolkit

156 4 2
saroudant
sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

153 6 2
kullrich
orthomap

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

69 6 1
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