Useful scripts for single-cell RNA-seq analysis

Overview

This repository stores scripts that can perform multiple aspects of the single-cell RNA-seq analysis. While an effort was made so that scripts could be broadly used, some of the parameters inevitably need to be adjusted by the user to reflect experimental designs or other sample-specific variables. In those cases, the scripts are well commented and should be easy to modify. Besides, this README file provides a brief description of each script and its usage.

Overall organization

For each analysis, a folder is created with the name of the analysis. Inside each folder, there is a README file that describes the analysis and the necessary scripts to perform it.

Available scripts

Converting data from Monocle3 object to Seurat object

The folder for this analysis is called "monocle3_to_seurat".

Trajectory inference with Slingshot

The folder for this analysis is called "trajectory_inference_using_slingshot".

Using COPILOT to analyze data from Cell Ranger

The folder for this analysis is called "COPILOT_using_CellRanger_output".