This repo contains code to reproduce the results and figures from the following preprint:
BRCA1 marks a proliferative developmental program co-opted in Group 3 and 4 medulloblastoma. Cheong I, Kishore N, Senff-Ribeiro A, Kim HS, Diaz-Navarro A, Sun X, Lau L, Hajari H, Mak E, Ahluwalia R, Bianchini L, Sandhu JS, Taylor MD, Kutscher L, Yaffe MJ, Stein LD, Pai S. bioRXiv preprint
- Pipeline to identify candidates for stalled differentiation:
01.Pipeline_StalledDifferentiation/01a.prioritizeCandidates.R - UMAPs from developing human rhombic lip:
01b.Aldinger_DimPlot_FeaturePlot.R
All code in 02.BrainDevelopment/
- Expression in Aldinger-Sepp, Nowakowski, and Braun datasets:
02[abc]*.R - PySCENIC analysis for BRCA1 regulon:
02[def]*.R - BrainSpan analysis:
02g.BrainSpanLi2018_BRCA1expr.R,02h.BrainSpanLi2018_general.R - PySCENIC for rhombic lip: This iPython notebook was too large to include in the github repository. It has been made available in the accompanying Zenodo repository (see link below).
- PySCENIC, plotting results, pathway analysis of BRCA1 regulon:
02d.AldingerPySCENIC_getBRCA1regulon.py,02e.Aldinger_plotRegulons.R,02f.AldingerPySCENIC_BRCA1regulonPathwayAnalysis.R
All code in 03.Medulloblastoma/
- Bulk RNA-seq analysis:
03a.Cavalli_BRCA1_Survival.R,03b.Cavalli_BRCA1.R - Count mutations in MB genomes using ICGC dataset:
03c.countMutationsInMB.R - Single-cell analysis of Vladoiu et al., CancerSEA :
03d.getCancerSEApathways.R,03e.Vladoiu_CancerSEA.R,03f.Vladoiu_FindMarkers.R - PySCENIC of Vladoiu et al. single-cell RNAseq: This iPython notebook was too large to include in the github repository. It has been made available in the accompanying Zenodo repository (see link below).
- PySCENIC, plotting results, pathway analysis of BRCA1 regulon:
03g.VladoiuPySCENIC_getBRCA1regulon.py,03h.Vladoiu_PlotRegulons.R,03i.VladoiuPySCENIC_BRCA1regulonPathwayAnalysis.R