BSgenome.Tcacao

R packages containing cacao reference genomes in bioconductor (BSgenome) format.

Installation steps

1. Install prerequisite R packages (devtools, BSgenome)
2. Install BSgenome.Tcacao packages from github

In R,

    # install devtools (if needed)
    install.packages("devtools")
    
    # install BSgenome from bioconductor
    source("https://bioconductor.org/biocLite.R")
    biocLite(c("BSgenome","VariantAnnotation","AnnotationDbi","GenomicFeatures"))
    
    # install Matina 1-6 reference genome package and accompanying gene model annotations
    devtools:::install_github("ConradStack/BSgenome.Tcacao/BSgenome.Tcacao.MarsInc.v11")
    devtools:::install_github("ConradStack/BSgenome.Tcacao/TxDb.Tcacao.Geneious.pub3i")

    # install Criollo reference genome
    devtools:::install_github("ConradStack/BSgenome.Tcacao/BSgenome.Tcacao.CIRAD.v10")