The folder simulation_scripts contains the scripts to do the simulations (generate_simu_DATASET.R), as well as the script to generate a reference with an additional artificial cell type. The simulations scripts will load a reference from a folder "references/" and create simulations with the date of the day in a folder called "simulations/"
The reference matrices used for the in silico data can be downloaded from Zenodo (DOI 10.5281/zenodo.14024479).
The table below recapitulates where to download in vitro and in vivo data.
| Dataset name | Source | Omic | Expression matrix | Proportion matrix | Reference profiles matrix |
|---|---|---|---|---|---|
| BlMIX | In vitro | DNAm | GSE77797 | Figure 4a (DOI: 10.1186/s12859-016-0943-7) | GSE35069 |
| BrMIX | In vitro | RNA | GSE220605 | "Cell count" column, table S1 (DOI: 10.1186/s13059-023-03016-6) | GSE220605 |
| PaMIX | In vitro | DNAm | GSE281305 | Zenodo (DOI: 10.5281/zenodo.14024479) | GSE281305 |
| PaMIX | In vitro | RNA | GSE281204 | Zenodo (DOI: 10.5281/zenodo.14024479) | GSE281204 |
| BlREAL1 | In vivo | RNA | https://github.com/Honchkrow/Deconer_dataset (Linsley.rds) | https://github.com/Honchkrow/Deconer_dataset (Linsley.rds) | https://github.com/Honchkrow/Deconer_dataset (Linsley.rds) |
| BlREAL2 | In vivo | DNAm | GSE35069 | DOI: 10.1371/journal.pone.0041361.s004 | GSE35069 |
| BlREAL3 | In vivo | DNAm | GSE42861 | Table S2 (DOI: 10.1038/nbt.2487) | GSE35069 |
| BlREAL3 | In vivo | RNA | GSE93722 | Supplementary file 3A (DOI: 10.7554/eLife.26476 ) | EPIC::TRef |