Search 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.

cytetype

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

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

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.

flashdeconv

Fast Linear Algebra for Scalable Hybrid Deconvolution of Spatial Transcriptomics

pybanksy

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

mudatasets

Multimodal datasets, in MuData format

ncem

ncem. Learning cell communication from spatial graphs of cells.

llm-sc-curator

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

flashs

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

sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

pycea-lineage

scverse lineage tracing analysis toolkit

orthomap

extract orthomap from OrthoFinder output for query species