This repository is designed to aid in the installation and running of single-cell RNA sequencing alignment protocols and to provide a starting point for advanced downstream analysis of scRNA-seq data.

• 📁 data-processing contains instructions for data alignment using a standard Cell Ranger protocol and kallisto pseudo-alignment protocol. To be added is Velocyto a toolkit that can be used for RNA velocity analysis.
• 📁 analysis contains the analysis code with some details regarding usage (NOTE: this section is very much still under development).

Outside of this repository, we also have a repository called, scrna-scripts which contains all the scripts and information for running preliminary analysis on a Cell Ranger aligned dataset. (NOTE: Still underdevelopment – expected to be finalized the week of 11/27/2023)