Repository for the code used in all computational analyses for the Ishida et al. 2023 submitted manuscript.
https://pubmed.ncbi.nlm.nih.gov/37333272/
The computational analysis was done in R using primarily Monocle3 and dependency packages. The sections of code used to create specific figure panels are designated in the comments of the file.
Figure 3.R contains code associated with Figure 3 for analysis of freshly sorted FL HSC data.
Figure 4.R contains code associated with Figure 4 for analysis of FL HSC co-cultured on stroma.
Figure 7-Nichnetr.R contains code associated with Figure 7 for analysis done with NicheNetR.
Figure 7-ReceptorLigand-pairs.R contains code associated with Figure 7 for analysis to identify novel receptor ligand interactions.
Raw data can be accessed through NCBI GEO at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233031
For questions regarding the code, please contact the corresponding author.