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. Author manuscript; available in PMC: 2022 Sep 22.
Published in final edited form as: Cell Syst. 2021 Aug 5;12(9):907–923.e6. doi: 10.1016/j.cels.2021.07.002

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Software and algorithms
R (version 3.6.3) Comprehensive R Archive Network (CRAN) https://www.r-project.org
RStudio (version 1.4.1106) RStudio: Integrated Development Environment for R http://www.rstudio.com/
clusterProfiler (3.12.0) CRAN https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
ComplexHeatmap (version 2.0.0) CRAN https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
Corrplot (version 0.84) CRAN https://cran.r-project.org/web/packages/corrplot/index.html
data.table (version 1.13.2) CRAN https://cran.r-project.org/web/packages/data.table/index.html
descr (version 1.1.4) CRAN https://cran.r-project.org/web/packages/descr/index.html
dplyr (version 1.0.2) CRAN https://cran.r-project.org/web/packages/dplyr/index.html
EnvStats (version 2.3.1) CRAN https://cran.r-project.org/web/packages/EnvStats/index.html
eulerr (version 6.1.0) CRAN https://cran.r-project.org/web/packages/eulerr/index.html
factoextra (version 1.0.7) CRAN https://cran.r-project.org/web/packages/factoextra/index.html
FactoMineR (version 2.3) CRAN https://cran.r-project.org/web/packages/FactoMineR/index.html
forcats (version 0.5.0) CRAN https://cran.r-project.org/web/packages/forcats/index.html
forestmodel (version 0.6.2) CRAN https://cran.r-project.org/web/packages/forestmodel/index.html
forestplot (version 1.10) CRAN https://cran.r-project.org/web/packages/forestplot/index.html
Hmisc (version 4.4–1) CRAN https://cran.r-project.org/web/packages/Hmisc/index.html
ggfortify (version 0.4.11) CRAN https://cran.r-project.org/web/packages/ggfortify/index.html
ggplot2 (version 3.3.2) CRAN https://cran.r-project.org/web/packages/ggplot2/index.html
ggpubr (version 0.4.0) CRAN https://cran.r-project.org/web/packages/ggpubr/index.html
ggsignif (version 0.6.0) CRAN https://cran.r-project.org/web/packages/ggsignif/index.html
ggthemes (version 4.2.0) CRAN https://cran.r-project.org/web/packages/ggthemes/index.html
gridExtra (version 2.3) CRAN https://cran.r-project.org/web/packages/gridExtra/index.html
KEGG.db (version 3.2.3) CRAN http://www.bioconductor.org/packages//2.11/data/annotation/html/KEGG.db.html
limma (version 3.40.6) CRAN https://bioconductor.org/packages/release/bioc/html/limma.html
missMDA (version 1.17) CRAN https://cran.r-project.org/web/packages/missMDA/index.html
org.Hs.eg.db (version 3.8.2) CRAN https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
RColorBrewer (version 1.1–2) CRAN https://cran.r-project.org/web/packages/RColorBrewer/index.html
ReactomePA (version 1.28.0) CRAN https://bioconductor.org/packages/release/bioc/html/ReactomePA.html
readr (version 1.4.0) CRAN https://cran.r-project.org/web/packages/readr/index.html
readxl (version 1.3.1) CRAN https://cran.r-project.org/web/packages/readxl/index.html
reshape2 (version 1.4.4) CRAN https://cran.r-project.org/web/packages/reshape2/index.html
scales (version 1.1.1) CRAN https://cran.r-project.org/web/packages/scales/index.html
stringr (version 1.4.0) CRAN https://cran.r-project.org/web/packages/stringr/index.html
survival (version 3.2–7) CRAN https://cran.r-project.org/web/packages/survival/index.html
survMisc (version 0.5.5) CRAN https://cran.r-project.org/web/packages/survMisc/index.html
survminer (version 0.4.8) CRAN https://cran.r-project.org/web/packages/survminer/index.html
tidyverse (version 1.3.0) CRAN https://cran.r-project.org/web/packages/tidyverse/index.html
vcd (version 1.4–8) CRAN https://cran.r-project.org/web/packages/vcd/index.html
Other
TCGA CNV dataset (thresholded) UCSC Xena https://tcga.xenahubs.net/download/TCGA.PANCAN.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes.gz
TCGA CNV dataset UCSC Xena https://tcga.xenahubs.net/download/TCGA.PANCAN.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes.gz
TCGA CNV ratio dataset UCSC Xena https://pancanatlas.xenahubs.net/download/broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena.gz
TCGA RNA-Seq dataset UCSC Xena https://pancanatlas.xenahubs.net/download/EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena.gz
TCGA sample type annotation UCSC Xena https://pancanatlas.xenahubs.net/download/TCGA_phenotype_denseDataOnlyDownload.tsv.gz
TCGA overall survival data UCSC Xena https://xenabrowser.net/datapages/?dataset=Survival_SupplementalTable_S1_20171025_xena_sp&host=https%3A%2F%2Fpancanatlas.xenahubs.net
TCGA and GTEX RNA-Seq dataset UCSC Xena https://toil.xenahubs.net/download/TcgaTargetGtex_RSEM_Hugo_norm_count.gz
TCGA and GTEX sample type annotation UCSC Xena https://toil.xenahubs.net/download/TcgaTargetGTEX_phenotype.txt.gz
CPTAC LUAD Sample Annotation (Gillette et al., 2020) https://cptc-xfer.uis.georgetown.edu/publicData/Phase_III_Data/CPTAC_LUAD_S046/CPTAC_LUAD_metadata/S046_BI_CPTAC3_LUAD_Discovery_Cohort_Samples_r1_May2019.xlsx
CPTAC LUAD Clinical Data (Gillette et al., 2020) https://cptc-xfer.uis.georgetown.edu/publicData/Phase_III_Data/CPTAC_LUAD_S046/CPTAC_LUAD_metadata/S046_BI_CPTAC3_LUAD_Discovery_Cohort_Clinical_Data_r1_May2019.xlsx
CPTAC LUAD RNA-Seq data (Gillette et al., 2020) https://www.cell.com/cms/10.1016/j.cell.2020.06.013/attachment/ab6fcc71–22e2–4ce9–9947-926fba367bd6/mmc2.xlsx
CPTAC LUAD proteomics data (Gillette et al., 2020) https://www.cell.com/cms/10.1016/j.cell.2020.06.013/attachment/49a46b71–468b-45d1–826a-721fa734eff0/mmc3.xlsx
CPTAC LUAD phosproteomics data (Gillette et al., 2020) https://www.cell.com/cms/10.1016/j.cell.2020.06.013/attachment/49a46b71–468b-45d1–826a-721fa734eff0/mmc3.xlsx
CCLE RNA-Seq data Broad https://ndownloader.figshare.com/files/27902091
CCLE proteomics data (Nusinow et al., 2020) https://gygi.hms.harvard.edu/data/ccle/protein_quant_current_normalized.csv.gz