Zero to Mouse Gastrulation Data

Summary

• Publication – https://pubmed.gov/30787436
• Shiny – https://marionilab.cruk.cam.ac.uk/MouseGastrulation2018
• Dataset – https://bioconductor.org/packages/MouseGastrulationData

Installation

• Only need to do once per container creation

# BiocManager::install( "MouseGastrulationData" )

Load packages

library( "MouseGastrulationData" )

library( "scran" )
library( "scater" )

Load data

sce <- EmbryoAtlasData( samples=29 )

snapshotDate(): 2020-10-27
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache

Normalize data

sce <- logNormCounts( sce )

Visualize expression

• Notch1

sce

class: SingleCellExperiment 
dim: 29452 7569 
metadata(0):
assays(2): counts logcounts
rownames(29452): ENSMUSG00000051951 ENSMUSG00000089699 ...
  ENSMUSG00000096730 ENSMUSG00000095742
rowData names(2): ENSEMBL SYMBOL
colnames(7569): cell_95727 cell_95728 ... cell_103294 cell_103295
colData names(17): cell barcode ... colour sizeFactor
reducedDimNames(2): pca.corrected umap
altExpNames(0):

plotReducedDim( sce, dimred="umap", colour_by="ENSMUSG00000033227" )

Document software

sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8

Matrix products: default
BLAS:   /home/idies/R/lib64/R/lib/libRblas.so
LAPACK: /home/idies/R/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] scater_1.18.6               ggplot2_3.3.3              
 [3] scran_1.18.7                MouseGastrulationData_1.4.0
 [5] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
 [7] Biobase_2.50.0              GenomicRanges_1.42.0       
 [9] GenomeInfoDb_1.26.7         IRanges_2.24.1             
[11] S4Vectors_0.28.1            BiocGenerics_0.36.1        
[13] MatrixGenerics_1.2.1        matrixStats_0.58.0         

loaded via a namespace (and not attached):
 [1] bitops_1.0-7                  bit64_4.0.5                  
 [3] httr_1.4.2                    tools_4.0.3                  
 [5] bslib_0.2.4                   utf8_1.2.1                   
 [7] R6_2.5.0                      irlba_2.3.3                  
 [9] vipor_0.4.5                   colorspace_2.0-0             
[11] DBI_1.1.1                     withr_2.4.2                  
[13] gridExtra_2.3                 tidyselect_1.1.1             
[15] bit_4.0.4                     curl_4.3.1                   
[17] compiler_4.0.3                BiocNeighbors_1.8.2          
[19] DelayedArray_0.16.3           labeling_0.4.2               
[21] sass_0.3.1                    scales_1.1.1                 
[23] rappdirs_0.3.3                stringr_1.4.0                
[25] digest_0.6.27                 rmarkdown_2.7                
[27] XVector_0.30.0                pkgconfig_2.0.3              
[29] htmltools_0.5.1.1             sparseMatrixStats_1.2.1      
[31] dbplyr_2.1.1                  fastmap_1.1.0                
[33] limma_3.46.0                  rlang_0.4.10                 
[35] RSQLite_2.2.7                 shiny_1.6.0                  
[37] DelayedMatrixStats_1.12.3     farver_2.1.0                 
[39] jquerylib_0.1.4               generics_0.1.0               
[41] jsonlite_1.7.2                BiocParallel_1.24.1          
[43] dplyr_1.0.7                   RCurl_1.98-1.3               
[45] magrittr_2.0.1                BiocSingular_1.6.0           
[47] GenomeInfoDbData_1.2.4        scuttle_1.0.4                
[49] Matrix_1.2-18                 ggbeeswarm_0.6.0             
[51] munsell_0.5.0                 Rcpp_1.0.6                   
[53] fansi_0.4.2                   viridis_0.6.1                
[55] lifecycle_1.0.0               stringi_1.5.3                
[57] yaml_2.2.1                    edgeR_3.32.1                 
[59] zlibbioc_1.36.0               BiocFileCache_1.14.0         
[61] AnnotationHub_2.22.1          grid_4.0.3                   
[63] blob_1.2.1                    promises_1.2.0.1             
[65] dqrng_0.2.1                   ExperimentHub_1.16.1         
[67] crayon_1.4.1                  lattice_0.20-41              
[69] cowplot_1.1.1                 beachmat_2.6.4               
[71] locfit_1.5-9.4                knitr_1.33                   
[73] pillar_1.6.0                  igraph_1.2.6                 
[75] glue_1.4.2                    BiocVersion_3.12.0           
[77] evaluate_0.14                 BiocManager_1.30.12          
[79] vctrs_0.3.8                   httpuv_1.6.0                 
[81] gtable_0.3.0                  purrr_0.3.4                  
[83] assertthat_0.2.1              cachem_1.0.4                 
[85] xfun_0.22                     rsvd_1.0.5                   
[87] mime_0.10                     xtable_1.8-4                 
[89] later_1.2.0                   viridisLite_0.4.0            
[91] tibble_3.1.1                  beeswarm_0.3.1               
[93] AnnotationDbi_1.52.0          memoise_2.0.0                
[95] bluster_1.0.0                 statmod_1.4.35               
[97] ellipsis_0.3.2                interactiveDisplayBase_1.28.0