Bioconductor review 1

[cvanderaa]

I updated the package based on the Bioconductor review. Here are the changes:

• README.md: extended the installation guide, providing both a stable and a devel installation.
• Removed the LazyLoad from the DESCRIPTION file and adapted the data loading (eg data(scp1) to data("scp1"))
• Documentation: added data collection description for the 3 example datasets
• Adapted the vignette to remove warnings and fix the PCA plot. However, I could not reproduce the missing plot. @lgatto, could you double-check that the PCA section seems correct (no warning and the PCA plot appears)?

[lgatto]

I get the following warning and issue with the PCA plot

this is with

> sessionInfo()
R Under development (unstable) (2020-04-28 r78328)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

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

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

other attached packages:
 [1] scp_0.99.2                  QFeatures_0.99.2           
 [3] MultiAssayExperiment_1.15.7 SummarizedExperiment_1.19.9
 [5] Biobase_2.49.1              GenomicRanges_1.41.6       
 [7] GenomeInfoDb_1.25.11        IRanges_2.23.10            
 [9] S4Vectors_0.27.14           BiocGenerics_0.35.4        
[11] MatrixGenerics_1.1.4        matrixStats_0.57.0         

loaded via a namespace (and not attached):
 [1] compiler_4.1.0              pillar_1.4.6               
 [3] BiocManager_1.30.10         XVector_0.29.3             
 [5] bitops_1.0-6                ProtGenerics_1.21.0        
 [7] tools_4.1.0                 zlibbioc_1.35.0            
 [9] SingleCellExperiment_1.11.8 lifecycle_0.2.0            
[11] tibble_3.0.4                lattice_0.20-41            
[13] pkgconfig_2.0.3             rlang_0.4.8                
[15] Matrix_1.2-18               DelayedArray_0.15.16       
[17] GenomeInfoDbData_1.2.4      dplyr_1.0.2                
[19] generics_0.0.2              vctrs_0.3.4                
[21] MsCoreUtils_1.1.7           tidyselect_1.1.0           
[23] grid_4.1.0                  glue_1.4.2                 
[25] R6_2.4.1                    purrr_0.3.4                
[27] AnnotationFilter_1.13.0     magrittr_1.5               
[29] ellipsis_0.3.1              MASS_7.3-51.6              
[31] RCurl_1.98-1.2              lazyeval_0.2.2             
[33] crayon_1.3.4