Prep Mouse Gastrulation Dataset

Summary

• Publication – https://pubmed.gov/30787436
• Shiny – https://marionilab.cruk.cam.ac.uk/MouseGastrulation2018
• Dataset – https://bioconductor.org/packages/MouseGastrulationData
• OSCA pipeline – http://www.c-moor.org/rnotebooks/osca-pbmc3k.nb.html

Load packages

BiocManager::install( "MouseGastrulationData" )
library( "MouseGastrulationData" )
library( "scran" )
library( "scater" )

Samples

AtlasSampleMetadata

Save Metadata and SCE Object

sce <- EmbryoAtlasData( )
df_meta <- data.frame( colData( sce ) )
write.table(df_meta, file = "~/workspace/Storage/C_MOOR/c_moor_ccc_fa21/gastrulation_meta.tsv", sep = "\t", row.names = FALSE)
save(sce, file = "~/workspace/Storage/C_MOOR/c_moor_ccc_fa21/gastrulation_sce.rda")

Document software

sessionInfo()