First of all, before cloning the BasCoD github package, go to the right directory that you would like to implement BasCoD. In the cmd terminal, do

cd {BasCoD directory}

then go on to the next step. {BasCoD directory} could be for example /storage10/kwangmoon/BasCoD.

For cloning the github repository, again on the cmd terminal, run the linux code

git clone https://github.com/keleslab/BasCoD.git

For R, we need the requirements as below :

• R: R installation (>=4.2.2)

In R, run those codes that download the required packages for running BasCoD.

install.packages('MASS')

Details about implementing codes and reproducing Figures in the manuscript can be found in the Tutorial of this github. There are mainly three tutorials provided:

• Tutorial 1: Mouse DS data
• Tutorial 2: Jerber et al. population scale scRNA-seq data
• Tutorial 3: HSPC erythroid differentiation analysis data
• Tutorial 4: Norman et al. Perturb-seq data with double perturbations

The required datasets can be found in the Google Drive link.