Scrna Seq Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

muon

muon is a multimodal omics Python framework

celltypist

A tool for semi-automatic cell type classification

palantir

Single cell trajectory detection

cirrocumulus

Bring your single-cell data to life

dynamo-release

Mapping Vector Field of Single Cells

doubletdetection

Doublet detection in single-cell RNA-seq data.

kb-python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

scarches

Reference mapping for single-cell genomics

tangram-sc

Spatial alignment of single cell transcriptomic data.

scvi

Deep probabilistic analysis of single-cell and spatial omics data

cellxgene

An interactive explorer for single-cell transcriptomics data

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

scdef

Deep exponential families for single-cell data.

desc

Deep Embedding for Single-cell Clustering

cellmapper

k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.

cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

irescue

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq

larry-dataset

Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning

scgen

Single cell perturbation prediction

symphonypy

Port of symphony algorithm of single-cell reference atlas mapping to Python

antipode

Variational Inference for Cell Type Evolution

mousipy

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

scplot

Single cell interactive plotting tools