| Deposited data |
|
| Clinical trial studies |
Clinicaltrials.gov |
https://clinicaltrials.gov/ |
| TCGA Omics data (Mutation/Copy number/RNA-seq/RPPA) |
UCSC Xena14
|
https://xenabrowser.net/datapages/?cohort=TCGA%20Pan-Cancer%20(PANCAN) |
| CCLE Omics data (Mutation/Copy number/RNA-seq/RPPA) |
UCSC Xena14
|
https://xenabrowser.net/datapages/?cohort=Cancer%20Cell%20Line%20Encyclopedia%20(CCLE) |
| Hallmark gene sets |
Molecular Signatures Database (MSigDB)15
|
http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp |
| Human DNA repair genes |
(Wood et al. 2005)16
|
https://www.mdanderson.org/documents/Labs/Wood-Laboratory/human-dna-repair-genes.html |
| Drug sensitivity for cell lines (IC50) |
Genomics of Drug Sensitivity in Cancer (GDSC)9
|
https://www.cancerrxgene.org/downloads/bulk_download |
| CIBERSORT Immune cell fraction (Methylation based) |
(Chakravarthy et al. 2018)17
|
https://doi.org/10.5281/zenodo.1298968 |
| CIBERSORT Immune cell fraction (RNA-seq based) |
(Thorsson et al. 2018)18
|
https://gdc.cancer.gov/about-data/publications/panimmune |
| The drug gene interaction database |
DGIdb19
|
https://www.dgidb.org/ |
| Census Genes Mutations |
COSMIC13
|
https://cancer.sanger.ac.uk/cosmic/download |
| Oncology Knowledge Base |
OncoKB20
|
https://oncokb.org |
|
| Software and algorithms |
|
| myCMIE |
This paper |
https://kowalski-labapps.dellmed.utexas.edu/CO3inW3/ |
| myCMIE Introduction |
The paper |
https://sites.utexas.edu/kowalski-muegge-lab-ut-austin/applications/w3/ |
| R (4.2.0) |
The R foundation |
https://www.r-project.org/ |
| R Shiny (1.7.3) |
Posit (RStudio) |
https://shiny.rstudio.com/ |
| enrichR |
Maayan lab |
https://maayanlab.cloud/Enrichr/ |
| ComplexHeatmap |
(Gu Z. 2022)21
|
https://github.com/jokergoo/ComplexHeatmap |
| chromoMap |
(Anand et al. 2022)22
|
https://github.com/cran/chromoMap |
| bookdown |
(Xie Y. 2016)23
|
https://github.com/rstudio/bookdown |
| MatchIt |
(Ho D. 2011)11
|
https://cran.r-project.org/web/packages/MatchIt/index.html |
