|
Deposited data
|
| CPTAC Pan-Cancer Data used in this study |
Li et al, accepted, Cancer Cell, CANCER-CELL-D-22–00603
|
https://kb.linkedomics.org/download
|
| GENCODE V34 basic (CHR) |
32
|
https://www.gencodegenes.org/human/release_34.html
|
| DrugBank version 5.1.9 |
33
|
https://go.drugbank.com
|
| Guide to Pharmacology version 2022.2 |
34
|
https://www.guidetopharmacology.org
|
| Cell Surface Protein Atlas |
35
|
https://wlab.ethz.ch/cspa/
|
| PhosphoSitePlus |
31
|
https://phosphosite.org
|
| Drug Gene Interaction Database version 2022-Feb |
36
|
https://www.dgidb.org
|
| Cancer Gene Census |
37
|
https://cancer.sanger.ac.uk/cosmic/download
|
| Tumor suppressor genes from Bailey et al |
38
|
Table S1
|
| Tumor suppressor genes from Tokheim et al |
39
|
Table S1
|
| PTMsigDB v1.9 |
40
|
https://github.com/broadinstitute/ssGSEA2.0/tree/master/db/ptmsigdb
|
| KinBase |
41
|
http://kinase.com/web/current/
|
| DEPOD |
42
|
http://www.depod.bioss.uni-freiburg.de/download.php
|
| CellTalkDB v1.0 |
43
|
https://github.com/ZJUFanLab/CellTalkDB
|
| Transcription factor database |
44
|
http://humantfs.ccbr.utoronto.ca
|
| DepMap: Pan-cancer essential genes |
45
|
https://depmap.org/portal/download/
|
|
Software and algorithms
|
| Metap v1.4 |
46
|
https://cran.r-project.org/web/packages/metap/index.html
|
| WebGestalt |
19
|
https://www.webgestalt.org
|
| GISTIC2.0 |
47
|
ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTIC_2_0_23.tar.gz
|
| ssGSEA 2.0 |
40
|
https://github.com/broadinstitute/ssGSEA2.0
|
| Strelka v2 |
48
|
https://github.com/Illumina/strelka
|
| MUTECT v1.7 |
49
|
https://software.broadinstitute.org/cancer/cga/mutect_download
|
| VarScan v2.3.8 |
50
|
http://dkoboldt.github.io/varscan/
|
| Pindel v0.2.5 |
51
|
https://github.com/genome/pindel
|
| CrossMap v0.5.3 |
52
|
https://crossmap.sourceforge.net/
|
| MutSigCV v1.41 |
53
|
https://software.broadinstitute.org/cancer/cga/mutsig
|
| ANNOVAR v04.16.2018 |
54
|
https://annovar.openbioinformatics.org/en/latest/
|
| CopywriteR v2.0.6 |
55
|
https://www.bioconductor.org/packages/release/bioc/html/CopywriteR.html
|
| CIRI v2.0.6 |
56
|
https://sourceforge.net/projects/ciri/
|
| BWA v0.7.17-r1188 |
57
|
https://bio-bwa.sourceforge.net/
|
| RSEM v1.3.1 |
58
|
http://deweylab.github.io/RSEM/
|
| Bowtie2 v2.3.3 |
59
|
https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| MSFragger v3.4 |
60
|
https://github.com/Nesvilab/MSFragger
|
| Philosopher v4.0.1 |
61
|
https://github.com/Nesvilab/philosopher
|
| TMT-Integrator v1.0.0 |
62
|
https://github.com/huiyinc/TMT-Integrator
|
| genomicWidgets |
10
|
https://github.com/bzhanglab/genomicWidgets
|
| maftools R package v2.10.0 |
63
|
https://bioconductor.org/packages/release/bioc/html/maftools.html
|
| Immunedeconv v2.0.4 |
64
|
https://github.com/omnideconv/immunedeconv
|
| CIBERSORT |
65
|
https://cibersortx.stanford.edu/
|
| xCell |
66
|
https://github.com/dviraran/xCell
|
| ESTIMATE |
67
|
https://bioinformatics.mdanderson.org/public-software/estimate/
|
| PROGENy v1.10.0 |
68
|
https://www.bioconductor.org/packages/release/bioc/html/progeny.html
|
| SigProfilerMatrixGeneratorR v1.0 |
69
|
https://github.com/AlexandrovLab/SigProfilerMatrixGeneratorR
|
| DoAbsolute v2.2 |
70
|
https://github.com/ShixiangWang/DoAbsolute
|
| ABSOLUTE v1.0.6 |
71
|
http://www.broadinstitute.org/cancer/cga/ABSOLUTE
|
| CNVEX |
16
|
https://github.com/mctp/cnvex
|
| Custom R scripts |
This paper |
https://doi.org/10.6084/m9.figshare.c.6690756
|
