TrajAtlas 0.2.1

TrajAtlas, a trajectory-centric framework reveals differentiation heterogenity among cells, genes, and gene modules

Unraveling multi-scale differentiation heterogeneity with trajectory-centric framework

TrajAtlas is a trajectory-centric framework designed to uncover heterogeneity among cells, genes, and gene modules across large-scale trajectories. It is applicable to, but not limited to, osteogenesis datasets. This repository contains the following modules:

• model: Enables users to project their datasets onto our Differentiation Atlas and predict lineage paths and pseudotime in the OPCST model.
• TrajDiff: Enable user to detect covariate-related differential cell abundance and genes along differentiation process across multiple trajectories.
• TRAVMap: enable user to detect pseudotemporal gene module and identified Trajectory-related Replicable Axes of Variation (TRAV)

Getting started

Please refer to the documentation. In particular:

• API documentation
• Tutorial

Installation

You need to have Python 3.8 or newer installed on your system. If you don't have Python installed, we recommend installing Mamba.

You can install TrajAtlas with following codes

pip install TrajAtlas

Citation

TrajAtlas recently has posted on bioRxiv. If TrajAtlas helps you, please cite our work.