R Notebook with scripts for running the bulk deconvolution and simulations.

You can find the following files in the repository:

1. R Notebook with examples: thymus_NPM-ALK_notebook.Rmd
2. Html with examples: thymus_NPM-ALK_notebook.html
3. Additional R functions: generic_functions.R
4. R file with the Bulk data object: eset.thymus.bulk.sparse.RData.zip

Libraries

In order to execute the complete pipeline, at the beginning of the R Notebook the following modified libraries must be installed:

1. SCDC:

   • Repository: https://github.com/crhisto/SCDC
   • Modifications:
     • Compatibility with sparse matrices using: dgCMatrix objects in R.
     • Routines with parallelization
     • Dynamic threshold for markers selection
     • Improvements in logs and so on.
   • Original repository: https://github.com/meichendong/SCDC

2. Biobase:

   • Repository: https://github.com/crhisto/Biobase.
   • Modifications: Compatibility with sparse matrices using: dgCMatrix objects in R.
   • Original repository: https://github.com/Bioconductor/Biobase

3. Xbioc:

   • Repository: https://github.com/crhisto/xbioc. Original repository:
   • Modifications: Compatibility with sparse matrices using: dgCMatrix objects in R.
   • Original repository: https://github.com/renozao/xbioc

Publication: Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis