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: CRC_organoids_and_fibroblasts_notebook.Rmd
2. Html with examples: CRC_organoids_and_fibroblasts_notebook.html
3. Additional R functions: generic_functions.R
4. Files with the Bulk data:
   • Count matrix: merged_rsem_counts_annotated.tsv.zip
   • Labels of samples: label_translation_samples.csv.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: Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model