Key resources table

RESOURCE	SOURCE	IDENTIFIER
Data Deposition
CPTAC clinical and proteomic data	CANCER-CELL-D-22-00603 companion Pan-Cancer resource manuscript	https://pdc.cancer.gov/pdc/cptac-pancancer
Full proteomic data tables - raw, harmonized and imputed	This manuscript	https://pdc.cancer.gov/pdc/cptac-pancancer
CPTAC genomic and transcriptomic data	CANCER-CELL-D-22-00603 companion Pan-Cancer resource manuscript	https://pdc.cancer.gov/pdc/cptac-pancancer, and Cancer Data Service (CDS)
Software and Algorithms
Somatic variant calling pipeline for CPTAC	Li Ding Lab	https://github.com/ding-lab/somaticwrapper
bam-readcount v0.8	McDonnell Genome Institute	https://github.com/genome/bam-readcount
GATK4’s CalculateContamination	GATK	https://gatk.broadinstitute.org/hc/en-us/articles/360036888972-CalculateContamination
GATK4 Picard tools	GATK	https://github.com/broadinstitute/picard
GATK4 Funcotator	GATK	https://gatk.broadinstitute.org/hc/en-us/articles/360037224432-Funcotator
Panel-Of-Normal token tool	Getz Lab	https://github.com/getzlab/tokenizer_TOOL
SNVmerge	Getz lab	https://github.com/getzlab/cptac_wxs_harmonize
Manta	Chen, X. et al., 2016 135	https://github.com/Illumina/manta
Strelka v2	Kim, S. et al., 2018 136	https://github.com/Illumina/strelka
MuTect	Cibulskis et al., 2013 137	https://software.broadinstitute.org/gatk/download/archive
DeTiN	Taylor-Weiner et al., 2018 138	https://github.com/getzlab/deTiN
VarScan2.3.8	Koboldt et al., 2012 139	http://varscan.sourceforge.net
Pindel0.2.5	Ye et al., 2009 140	http://gmt.genome.wustl.edu/packages/pindel/
SignatureAnalyzer	Kim et al., 2016 30	https://github.com/getzlab/getzlab-SignatureAnalyzer
GISTIC2.0	Mermel et al.,2011 141	https://github.com/broadinstitute/gistic2
MutSig2CV	Lawrence et al., 2014 142	https://github.com/getzlab/M utSig2CV
GTEx RNA-seq pipeline	The GTEx Consortium, 2020 143	https://github.com/broadinstitute/gtex-pipeline
CLUMPS-PTM	Getz lab	https://github.com/getzlab/CLUMPS-PTM
The Kinase Library	Johnson et al.,2022 33	Described in Methods
CausalPath	Babur et al.,202134	https://github.com/PathwaAndDataAnalysis/causalpath
Spectrum Mill	Karl R. Clauser, Steven Carr Lab	https://proteomics.broadinstitute.org/
ComBat (v3.20.0)	Johnson, Li and Rabinovic, 2007 144	https://bioconductor.org/packages/release/bioc/html/sva.html
ESTIMATE	Yoshihara et al., 2013 71	https://bioinformatics.mdanderson.org/public-software/estimate/
fGSEA	Subramanian, Tamayo, et al., 2005 145	http://bioconductor.org/packages/release/bioc/html/fgsea.html
GSVA	Hänzelmann S, et al., 2013 146	https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
xCell	Aran, Hu and Butte,2017 147	http://xcell.ucsf.edu/
PepQuery	Wen, Wang and Zhang, 2019 148	http://pepquery.org
PTM-SEA	Krug et al.,2019 35	https://github.com/broadinstitute/ssGSEA2.0
Terra	Broad Institute data science platform.	https://terra.bio/
LIMMA v3.36 (R Package)	Ritchie et al., 2015 149	https://bioconductor.org/packages/release/bioc/html/limma.html
Other