Single Cell Rna Seq Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

squidpy

Spatial Single Cell Analysis in Python

liana

LIANA+: an all-in-one framework for cell-cell communication

cellrank

CellRank: dynamics from multi-view single-cell data

divik

Divisive Intelligent K-Means algorithm (DiviK) for joint feature selection and clustering of heavily multidimensional data.

kb-python

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

sccoda

A Bayesian model for compositional single-cell data analysis

scvi

Deep probabilistic analysis of single-cell and spatial omics data

scdataloader

a dataloader to work with large single cell datasets from lamindb

scdef

Deep exponential families for single-cell data.

scxpand

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

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.

scxpand-cuda

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

toolchest-client

Python client for Toolchest

cello-classify

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

nichenetpy

nichenetpy: the python implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

irescue

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

scvelo-rs

Drop-in Rust acceleration of scVelo for single-cell RNA velocity.

emergene

Individual cell-based differential transcriptomic analysis across conditions

scmalignantfinder

scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells from their normal counterparts.

cosg

Accurate and fast cell marker gene identification with COSG

cell-blast

Single-cell transcriptome querying tool

scdrs

Single-cell disease relevance score (scDRS)