notes_installation.txt

# manual installations:

# for SingleR
install.packages("pbmcapply")
devtools::install_github('dviraran/SingleR')
# OBS! without updating any of the packages.


# for CHETAH
devtools::install_github("asabjorklund/CHETAH")

# OBS! without updating any of the packages.
# OBS! original github repo has R>=3.6 in Description, works fin to install from my fork with R 3.5.1
# Should be installed from: "jdekanter/CHETAH"



###################################################

SingleR - https://github.com/dviraran/SingleR
Imports: BiocManager, - installed
    RColorBrewer, - installed
    outliers, - fix
    matrixStats, - installed
    plyr, - installed
    dplyr, - installed
    ggplot2, - installed
    pbmcapply, - fix
    Matrix, - installed
    GSEABase, - fix
    GSVA, - fix
    pheatmap, - installed
    parallel,- installed
    devtools, - installed
    doFuture, - fix
    data.table, - installed
    foreach, - installed
    singscore, - fix
    doParallel - - installed

# all but pbmcapply have conda env.
- pbmcapply compilation errors req MacOSX SDKs insalled.
# open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg &


CHETAH - https://github.com/jdekanter/CHETAH
# OBS! Says R>=3.6
Imports:
    gplots, - installed
    shiny, - installed
    plotly, - installed
    pheatmap, - installed
    bioDist,  - fix
    dendextend, - fix 
    cowplot,- installed 
  	corrplot, - fix
  	grDevices, - installed
  	stats, - installed
  	graphics, - installed
  	reshape2, - installed
  	S4Vectors, - installed 
  	SummarizedExperiment - installed
Depends:
    R (>= 3.6),
	  ggplot2, - installed
  	SingleCellExperiment - installed