| Deposited data |
| TCGA level 4 RNA-seq, clinical and survival information (LUAD, LUSC and SKCM samples) |
UCSC Xena database |
https://gdc.xenahubs.net |
| TCGA level 3 somatic mutation data (LUAD, LUSC and SKCM samples) |
Genomic Data Commons |
https://portal.gdc.cancer.gov/ |
| TCGA RPPA data (LUAD, LUSC and SKCM samples) |
RPPA Core Facility, MD Anderson Cancer Center |
http://app1.bioinformatics.mdanderson.org/tcpa/_design/basic/index.html |
| TCGA HLA allele information (LUAD, LUSC and SKCM samples) |
The Cancer Immunome Atlas |
https://tcia.at/home |
| TCGA fusion genes (LUAD, LUSC and SKCM samples) |
ChimerDB 4.0 database |
https://www.kobic.re.kr/chimerdb/ |
| Raw WES data (Rizvi LUAD and Synder melanoma samples) |
Database of Genotypes and Phenotypes |
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000980.v1.p1 |
| https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001041.v1.p1 |
| Raw RNA-seq and WES data (Amato melanoma samples) |
NCBI Sequence Read Archive database |
https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP267584 |
| https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP217040 |
| Raw and processed RNA-seq and WES data (Abbott melanoma samples) |
Database of Genotypes and Phenotypes |
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002388.v1.p1 |
| NCBI Gene Expression Omnibus |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15996 |
| Raw and processed RNA-seq and WES data (SMC NSCLC samples) |
NCBI Sequence Read Archive database |
https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP217040 |
| NCBI Gene Expression Omnibus |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203360 |
| European Genome-phenome Archive |
https://ega-archive.org/datasets/EGAD00001005211 |
| Processed single-cell RNA-seq data (NSCLC and melanoma samples) |
NCBI Gene Expression Omnibus |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17794 |
| https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575 |
| Software and algorithms |
| R v4.1.0 |
The Comprehensive R Archive Network |
https://www.r-project.org/ |
| BWA v0.7.15 |
|
http://bio-bwa.sourceforge.net/ |
| MuTect2 v4.1.0 |
|
https://github.com/broadinstitute/mutect |
| GATK v4.1.7.0 |
Van et al. [9] |
https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/ |
| Polysolver |
Shukla et al. [44] |
https://github.com/jason-weirather/hla-polysolver |
| NetMHCpan v4.1 |
Reynisson et al. [46] |
https://services.healthtech.dtu.dk/service.php?NetMHCpan-4.1 |
| deepHLApan v1.1 |
Wu et al. [47] |
https://github.com/jiujiezz/deephlapan |
| STAR v2.7.9a |
|
https://github.com/alexdobin/STAR |
| STAR-Fusion v1.10.1 |
Haas et al. [62] |
https://github.com/STAR-Fusion/STAR-Fusion |
| Arriba v2.2.1 |
|
https://github.com/suhrig/arriba |
| GeneFuse v0.6.1 |
|
https://github.com/OpenGene/genefuse |
| CNVkit v0.9.7 |
|
https://github.com/etal/cnvkit |
| TRUST4 v1.0.6 |
Song et al. [51] |
https://github.com/liulab-dfci/TRUST4 |
| Seurat v4.2.0 |
Hao et al. [63] |
https://satijalab.org/seurat/ |
| CIBERSORTx |
Newman et al. [53] |
https://cibersortx.stanford.edu/runcibersortx.php |
| ABSOLUTE v1.0.6 |
|
https://software.broadinstitute.org/cancer/cga/absolute |
| xCell v1.1.0 |
Aran et al. [52] |
https://github.com/dviraran/xCell/ |
| LOHHLA |
McGranahan et al. [12] |
https://bitbucket.org/mcgranahanlab/lohhla/src/master/ |
| survminer v0.4.9 |
The CRAN package repository |
https://cran.r-project.org/package=survminer |
| survival v3.2.11 |
The CRAN package repository |
https://cran.r-project.org/package=survival |
| factoextra v1.0.7 |
The CRAN package repository |
https://cran.r-project.org/package=factoextra |
| clusterProfiler v4.1.4 |
Yu et al. [56] |
http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| fgsea v1.20.0 |
Sergushichev et al. [48] |
http://bioconductor.org/packages/release/bioc/html/fgsea.html |
| GSVA v1.40.0 |
Hänzelmann et al. [61] |
https://bioconductor.org/packages/release/bioc/html/GSVA.html |
