This repository is the accompanying code for our paper on the development of extraembryonic ectoderm and embryonic tissues during mouse gastrulation. There is an MCView shiny app where you can interrogate the data. The code is splitted into jupyter notebooks that can be found in the notebook folder.
Prior to any analysis, after cloning the repository, please download first the necessary data by running (in the root directory of the cloned repository):
R -e "source('scripts/download_data.R'); download_full_data()"This will download all the necessary data including processed metacell objects necessary for generating the figures. The subfolder data/umi.tables contains all the UMI matrices of the scRNA-seq data used in the paper.
The initialization script (scripts/init.R) loads automatically the necessary R packages to run the notebooks. The analysis was done using R 4.0.5 and the following packages:
- devtools_2.4.2
- usethis_2.0.1
- here_1.0.1
- slanter_0.2-0
- DoubletFinder_2.0.3
- SeuratObject_4.0.2
- Seurat_4.0.3
- forcats_0.5.1
- stringr_1.4.0
- dplyr_1.0.9
- purrr_0.3.4
- readr_2.1.0
- tidyr_1.2.0
- tibble_3.1.3
- ggplot2_3.3.5
- tidyverse_1.3.1
- umap_0.2.7.0
- tgutil_0.1.13
- tgstat_2.3.17
- metacell_0.3.7
- Matrix_1.3-4
- data.table_1.14.2
- qvalue_2.22.0
- princurve_2.1.6
- RColorBrewer_1.1-2
- tglkmeans_0.3.4
- zoo_1.8-9
- ggrepel_0.9.1
For every Figure there is a corresponding notebook that generates the plots shown in the figure. By running the notebooks below in the specified order, one can reproduce the whole analysis of the paper starting from the scRNA-seq UMI matrices.
For reproducing the analysis of the wildtype ExE and embryonic manifold you should run the following notebooks in that order.
- import_mars
- embexe_find_bad_genes
- embexe metacell construction
- embryo_temporal_ordering
- embexe_interpolate_time
- mc2d_projection_embexe
- split_embexe_into_emb_and_exe
- emb.estimation_of_proliferation_rates
- emb_generate_network
- mc2d_projection_emb
- mc2d_projection_exe
- import_elf5
- elf5_processing_summary
- import_10x_exutero
- exutero_doublet_removal
- exutero_f_find_bad_genes
- exutero_f_generate_metacell
- mc2d_projection_exutero_f
- wt_atlas_projection_of_exutero_embryos
- atlas_self_projection_of_wt_cells