| Deposited Data |
| Raw germline data |
NCI Genomic Data Commons |
https://portal.gdc.cancer.gov/ |
| Haplotype Reference Consortium |
McCarthy et al., 2016 |
http://www.haplotype-reference-consortium.org/ |
| 1000 Genomes Project |
Auton et al., 2015 |
https://www.internationalgenome.org/ |
| Immune cellular fraction estimates and immune gene expression signatures |
Thorsson et al., 2018 |
https://gdc.cancer.gov/about-data/publications/panimmune |
| Cytolytic activity calculation |
Rooney et al., 2015 |
PMID: 25594174 |
| Celiac disease GWAS summary statistics |
Dubois et al., 2010 |
PMID: 20190752 |
| Multiple sclerosis GWAS summary statistics |
Sawcer et al., 2011 |
PMID: 21833088 |
| Rheumatoid arthritis GWAS summary statistics |
Okada et al., 2014 |
PMID: 24390342 |
| Systemic lupus erythematosus GWAS summary statistics |
Bentham et al., 2015 |
PMID: 26502338 |
| Ulcerative colitis GWAS summary statistics |
Anderson et al., 2011 |
PMID: 21297633 |
| HINT |
Das and Yu, 2012 |
http://hint.yulab.org/ |
| HI |
Rolland et al., 2014 |
http://www.interactome-atlas.org/download |
| iRefIndex |
Razick et al., 2008 |
https://irefindex.vib.be/download/irefindex/data/archive/release_15.0/psi_mitab/MITAB2.6/9606.mitab.22012018.txt.zip |
| ReactomeFI 2016 |
Fabregat et al., 2018 |
https://reactome.org/ |
| Software and Algorithms |
| Admixture |
Alexander et al., 2009 |
http://software.genetics.ucla.edu/admixture/ |
| Birdseed |
Korn et al., 2008 |
https://www.broadinstitute.org/birdsuite/birdsuite-analysis |
| Hierarchical HotNet |
Reyna et al., 2018 |
https://github.com/raphael-group/hierarchical-hotnet |
| METAL |
Wilier et al., 2010 |
https://genome.sph.umich.edu/wiki/METAL |
| Michigan Imputation Server |
Das et al., 2016 |
http://imputationserver.sph.umich.edu/index.html |
| PEGASUS |
Nakka et al., 2016 |
https://github.com/ramachandran-lab/PEGASUS |
| plink |
Chang et al., 2015 |
https://www.cog-genomics.org/plink2/ |
| PRSice |
Euesden et al., 2015 |
http://www.prsice.info/ |
