Scanpy Python Packages

anndata

Annotated data.

scanpy

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

muon

muon is a multimodal omics Python framework

anndata2ri

Convert between AnnData and SingleCellExperiment

cirrocumulus

Bring your single-cell data to life

adpbulk

pseudobulking on an AnnData object

checkatlas

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

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

cytetype

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

fgread

Python readers for different data formats for FASTGenomics.

treedata

anndata with trees

mllmcelltype

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

mousipy

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

pybanksy

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

flashdeconv

Fast Linear Algebra for Scalable Hybrid Deconvolution of Spatial Transcriptomics

mudatasets

Multimodal datasets, in MuData format

llm-sc-curator

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

ncem

Learning cell communication from spatial graphs of cells

flashs

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

pycea-lineage

scverse lineage tracing analysis toolkit

sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

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.