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

cytotable

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

celescope

Single Cell Analysis Pipelines

spacr

spaCR Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR)

spatialprofilingtoolbox

Toolbox for spatial analysis of single cell data.

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

featuremap

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

emergene

Individual cell-based differential transcriptomic analysis across conditions

scportrait

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

cosg

Accurate and fast cell marker gene identification with COSG

sctape

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

spacr-nightly

Spatial phenotype analysis of crisp screens (SpaCr)

transmorph

A unifying data integration framework.

pypairs

A python scRNA-Seq classifier

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

vipcca

single cell integration

ccsf

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

pyspade

Single cell Perturbations - Analysis of Differential gene Expression

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

icat-sc

Identifying Cell-states Across Treatments

laris

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