Create container for NeuroCogII tutorial

[Loyale]

Avoid having the issue(s) associated with installations and missing files.

`# Install devtools if it's not already installed
if (!require(devtools)) {
install.packages("devtools")
}

Install from GitHub

devtools::install_github("mannau/h5")
devtools::install_github("BUStools/BUSpaRse")
devtools::install_github("satijalab/seurat-wrappers")
devtools::install_github("LTLA/SingleR")
devtools::install_github('linxihui/NNLM')
devtools::install_github('cvarrichio/Matrix.utils')

if (!require(BiocManager)) {
install.packages("BiocManager")
BiocManager::install(c("DropletUtils", "BSgenome.Mmusculus.UCSC.mm10",
"AnnotationHub", "SingleR","biomaRt","tidyverse","scales","zeallot","densityClust"))
}

if (!require(monocle3)) {
BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
'limma', 'S4Vectors', 'SingleCellExperiment',
'SummarizedExperiment', 'batchelor','fgsea'))
devtools::install_github('cole-trapnell-lab/leidenbase') # clustering package dependency for monocle3
devtools::install_github('cole-trapnell-lab/monocle3')
devtools::install_github('scfurl/m3addon') # Monocle3 addon functions from scfurl (optionally included to illustrate high-variance gene identification)
}

if (!require(velocyto.R)) {
BiocManager::install(c("pcaMethods"))
devtools::install_github("velocyto-team/velocyto.R")
}
`

• 10X 10K

# Download data if (!file.exists("./data/neuron_10k_v3_fastqs.tar")) { download.file("http://s3-us-west-2.amazonaws.com/10x.files/samples/cell-exp/3.0.0/neuron_10k_v3/neuron_10k_v3_fastqs.tar", "./data/neuron_10k_v3_fastqs.tar", method = "wget", quiet = TRUE) }