TrajAtlas 0.1.3

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.