1 The intrinsic and extrinsic effects of Tet proteins during gastrulation

Following is the code that generates the figures of our paper on TET function during gastrulation. The code is splitted to jupyter notebooks that can be found at: https://github.com/tanaylab/tet-gastrulation

1.1 Run the notebooks

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. You can also download a minimal version ( download_minimal_scrna_data() ) in which case you would need to rerun all the notebooks prior to generate-figures (see section Notebook order below.)

1.2 Necessary R packages

You can install the necessary R packages by running:

remotes::install_github("tanaylab/tet-gastrulation", subdir = "scripts/tet.gastru")

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:

  • gridExtra 2.3
  • qvalue 2.22.0
  • ggrepel 0.9.1
  • ggpubr 0.4.0
  • ggplot2 3.3.5
  • zoo 1.8-9
  • qlcMatrix 0.9.7
  • sparsesvd 0.2
  • slam 0.1-49
  • tidyr 1.2.0
  • dplyr 1.0.9
  • tgutil 0.1.13
  • tgstat 2.3.17
  • metacell 0.3.7
  • Matrix 1.3-4

1.3 Notebook order

You should run the notebooks import_plates and gating first and generate-figures last.

  1. import_plates
  2. gating
  3. TKO-chimera-embryos-processing
  4. TKO-tetraploid-complemented-embryos-processing
  5. Control-tetraploid-complemented-embryos-processing
  6. DKO-chimera-embryos-processing
  7. AAV_Cre-TKO-embryos-processing
  8. Methylation
  9. generate-figures