Single Cell Analysis Python Packages

harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

scimap

Spatial Single-Cell Analysis Toolkit

pycomplexheatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

qpsphere

Python library for spheres in quantitative phase imaging

celescope

Single Cell Analysis Pipelines

spacr

Spatial phenotype analysis of crisp screens (SpaCr)

cytotable

Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.

spacr-nightly

Spatial phenotype analysis of crisp screens (SpaCr)

spatialprofilingtoolbox

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

scportrait

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

pypairs

PyPairs - A python scRNA-Seq classifier

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

sctape

deep learning tools for bulk RNA-seq deconvolution and gene expression analysis

cosg

Accurate and fast cell marker gene identification with COSG

transmorph

A unifying data integration framework.

mnnpy

Mutual nearest neighbors correction in python.

emergene

EMERGENE for individual cell-based differential transcriptomic analysis across conditions.

featuremap

FeatureMAP (Feature-preserving Manifold Approximation and Projection) is an interpratable dimensionality reduction tool.

vipcca

single cell integration

ccsf

Leveraging cell-cell similarity from gene expression data for high-performance spatial and temporal cellular mappings.

scslat

A graph deep learning based tool to align single cell spatial omics data

laris

LARIS enables accurate and efficient ligand and receptor interaction analysis in spatial transcriptomics

scouts

Single Cell Outlier Selector

sckinetics

Biological prior guided single-cell kinetics inference.