title	author	date	output
scRNASeq Prostate Cancer	Alex Germanos, Sonali Arora	January 18, 2022	html_document toc theme true united

Introduction

This github repository contains code to reproduce the analysis in our upcoming paper "Defining cellular population dynamics at single cell resolution during prostate cancer progression" from the Hsieh Lab at Fred Hutch Cancer Center.

Tools used for the Analysis

1. SingleCellExperiment for processing scRNASeq data
2. Seurat for processing scRNASeq data
3. SingleR for performing unbiased cell type recognition
4. velocyto.R for RNA velocity analysis
5. Monocle for trajectory analysis
6. Palantir for trajectory analysis
7. ggplot2 for making figures
8. GSVA for GSVA analysis
9. pheatmap for making heatamps
10. RColorBrewer for color-scheme palettes