README.md

HEOA: human Early Organogenesis Atlas

1. This repository contains the R code used in the following paper on human emrbyo:

A single cell transcriptome atlas of human early embryogenesis

2. The introduction for file structure

1. src/: source codes for each figure (corresponding to *.html) and all other analysis (e.g., identification of cell types and identification of systemically changing genes). All custom functions were stored in 'function.r' and 'functions.r'.
2. data/: necessary input data for scripts: gene annotation, cell annotation, color scheme, and contours of limb domains.
3. list/: gene list from published data: batch effect genes, cell cycle genes, and hemoglobin genes.
4. plot/: figures generated in the analysis that are not included in R markdown files.
5. remap_Tan_frog: the script to map RNA-seq data of frog embryos (Tan et al. 2013) on latest frog genome.

3. An online depository for cell types and gene expression is avaiable at https://heoa.shinyapps.io/base/.

4. The raw and processed data can be downloaded from the NCBI Gene Expression Omnibus (GSE157329).