RetinalGanglionCell-ONC

Here we provide the source code and an Rmarkdown tutorial to reproduce the survival analysis of mouse retinal ganglion cells (RGCs) following optic nerve crush. RGCs are the projection neurons of the retina, and we identified 45 molecular groups of adult RGCs in mice.

Here, adult mouse RGCs were profiled using single-cell RNA-seq at 6 time points following optic nerve crush. We devised a procedure that we called iGraphBoost that maps injured RGCs to each of 45 types based on their transcriptomic signature. The steps underlying the procedure are described in Tran^*, Shekhar^*, Whitney^*, Jacobi^* et al., Neuron, 2019.

iGraphBoost.R contains the source code for this analysis. We are preparing an Rmarkdown file detailing all the steps. In the meantime the data presented in the paper can be explored on the Broad Institute's Single Cell portal,

https://singlecell.broadinstitute.org/single_cell/study/SCP509/mouse-retinal-ganglion-cell-adult-atlas-and-optic-nerve-crush-time-series

Please shoot an e-mail to [email protected] for any questions.