Scrna Seq Analysis Python Packages

palantir

Single cell trajectory detection

meld

Quantifying experimental perturbations at single cell resolution

scarf

Memory-efficient single-cell analysis in Python. Stream RNA, ATAC, CITE-seq and multi-omics from local or remote Zarr stores, from laptop to atlas scale, with reusable fingerprinted results.

polariseq

Atlas-scale single-cell RNA-seq analysis in Python with a Rust core. Plans memory before reading; runs in memory or out of core.

stcat

The single T cell annotation tool for scRNA-seq data

sccausalvi

Perturbational analysis by causality-aware generative model for single-cell RNA-sequencing data

cytearc

Fast, out-of-core single-cell analysis in Python for RNA, ATAC, protein, and multi-omic data, scaling to 100M+ cells. Mount remote datasets, work within a memory budget, and trace every result through built-in provenance.

scregulate

Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data

pypairs

PyPairs - A python scRNA-Seq classifier

sctreeshap

An effective tool for single-cell RNA sequencing.

airqtl

Single-cell eQTL mapping and causal gene regulatory network inference at high efficiency and accuracy

harmonyts

Harmony framework for connecting scRNA-seq data from discrete time points

scvital

Deep Learning Algorithm for cross-species integration of scRNA-seq data

pyscalr

Single cell analysis using Low Resource

northstar

Single cell type annotation guided by cell atlases, with freedom to be queer

orthomap

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

swnn

Constructing a developmental tree from scRNA-seq data

scomix

Single-Cell Data Science