| Deposited data |
|
| eRNA data |
https://hanlab.uth.edu/eRic/ |
eRic |
| TCGA-STAD RNA-seq |
https://portal.gdc.cancer.gov/ |
TCGA |
| Somatic mutation data |
https://xenabrowser.net/datapages/ |
UCSC Xena |
| TCGA-STAD clinical data |
https://xenabrowser.net/datapages/ |
UCSC Xena |
| GENECODE V22 |
https://www.gencodegenes.org/ |
GENECODE |
| Somatic copy number data |
https://gdac.broadinstitute.org/ |
Broad GDAC Firehouse |
| SNP data |
https://portal.gdc.cancer.gov/ |
TCGA |
| GC validation set |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15459 |
GEO: GSE15459
|
| GC validation set |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34942 |
GEO: GSE34942
|
| GC validation set |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62254 |
GEO: GSE62254
|
| GC validation set |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84437 |
GEO: GSE84437
|
| GC validation set |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13861 |
GEO: GSE13861
|
| GC validation set |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26901 |
GEO: GSE26901
|
| GC validation set |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93157 |
GEO: GSE93157
|
| meta-melanoma cohort |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78220 |
GEO: GSE78220
|
| meta-melanoma cohort |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE91061 |
GEO: GSE91061
|
| meta-melanoma cohort |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100797 |
GEO: GSE100797
|
| meta-melanoma cohort |
https://aacrjournals.org/cancerimmunolres/article/5/1/84/468570/Somatic-Mutations-and-Neoepitope-Homology-in |
melanoma cohort from Nathanson et al |
|
| Software and algorithms |
|
| R (v4.0.0) |
R Core Team |
https://www.r-project.org/ |
| ssGSEA |
GSVA R package |
http://www.bioconductor.org |
| pRRophetic |
Geeleher P et al., 2 014 |
http://genemed.uchicago.edu/pgeeleher/pRRophetic |
