Tooth_sciRNAseq

This repository contains the R codes used for the paper (Human iPSC Derived Enamel Organoid Guided by Single Cell Atlas of Human Tooth Development)

System requirements:

All codes were tested on Windows 10 (R version 4.1.1) and Linux running R (version 3.6.3), and Python (version 3.7).

Installation:

Monocle3

To install monocle3 Please follow the instructions provided in the Trapnell-lab website https://cole-trapnell-lab.github.io/monocle3/docs/installation/

scMLnet

Please follow the instructions provided by this package authors to install the python and R components https://github.com/SunXQlab/scMLnet

talklr

library(devtools)
install_github("yuliangwang/talklr")

other dependencies

install.packages(c('Seurat', 'treemap', 'networkD3','hrbrthemes', 'viridis', 'patchwork', 'circlize','tidyverse','tidyr','rliger','pheatmap','stringr', 'igraph','RColorBrewer','gridExtra','reshape2','ggtext'))

Other Bioconductor dependencies

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.10")
BiocManager::install(c("DEsingle","ComplexHeatmap","ViSEAGO","simplifyEnrichment","BiocParallel"))

Instructions

The instructions to run each function are written as comments in the each R script file.

Top_pathway.R

This file contains the main workflow to identify the top pathway activities at each step of ameloblast differentiation.

Customized_heatmap.R

This file contains the instruction to use the customized heatmap function that utilizes the complexHeatmap package, and combines key goterms and age_score calculations per cluster.

Realtime_heatmap.R

This file contains the instructions to use the realtime heatmap function to show expression of a single gene over timepoints that can be compared across clusters.

RNAScope_AM.R & RNAScope_OB.R

These files contain the code to generate the RNAScope maps for both ameloblasts and odontoblasts.