Cell biology Tools

COSG is a cosine similarity-based method for more accurate and scalable marker gene identification.

A fast and versatile toolkit for accurate de novo assembly of organelle genomes. This toolkit assemblies organelle genome from genomic skimming data.

Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets.

Epigenomics Single Cell Analysis in Python.

Sinto is a toolkit for processing aligned single-cell data.