| Deposited data |
|
| Mouse immunopeptidomics |
Schuster et al. (2018) |
https://doi.org/10.1038/sdata.2018.157 |
| Human immunopeptidomics |
Marcu et al. (2021) |
https://doi.org/10.1136/jitc-2020-002071 |
| Mouse proteomics |
Geiger et al. (2013). doi: https://doi.org/10.1074/mcp.M112.024919. Epub 2013 Feb 22. PMID: 23436904; PMCID: PMC3675825 |
https://doi.org/10.1074/mcp.m112.024919 |
| Mouse transcriptomics |
Söllner et al. (2017) |
https://doi.org/10.1038/sdata.2017.185 |
Human transcriptomics (accessed January 10th 2020), the dataset used was: ‘GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_
gene_median_tpm.gct’ |
GTEX repository https://www.gtexportal.org/home/(accessed January 10th 2020) |
GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_
gene_median_tpm.gct |
| Human proteomics |
Wang et al. (2019). doi: https://doi.org/10.15252/msb.20188503. PMID: 30777892; PMCID: PMC6379049 |
https://doi.org/10.15252/msb.20188503 |
| PhastCons Gene conservation data (Human) |
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/(accessed June 5th 2020) |
DOI:https://doi.org/10.18129/B9.bioc.TxDb.Hsapiens.UCSC.hg38.knownGene
|
| PhastCons Gene conservation data (Mouse) |
http://hgdownload.soe.ucsc.edu/goldenPath/mm10/multiz60way/(accessed June 5th 2020) |
DOI: https://doi.org/10.18129/B9.bioc.TxDb.Mmusculus.UCSC.mm10.knownGene
|
|
| Software and algorithms |
|
| R |
https://www.r-project.org/ |
|
| R Studio |
https://www.rstudio.com/ |
|
| MHC-I Atlas |
In-house code |
https://github.com/CaronLab/MHCIatlas |
