REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Tumor biopsy before treatment	I-SPY 2 TRIAL	https://clinicaltrials.gov/ct2/show/NCT01042379
Critical commercial assays
Reverse phase protein array (RPPA)	Petricoin Lab, George Mason University	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL28470
Deposited data
Raw and processed RPPA data	This study	Gene Expression Omnibus (GEO) SubSeries GSE196093 (RPPA) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196093, as part of the SuperSeries GSE196096 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196096); and in the I-SPY 2 Google Cloud repository (http://www.ispytrials.org/results/data)
Patient-level expression signature and clinical data	This study	Gene Expression Omnibus (GEO) SuperSeries GSE196096 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196096); and in the I-SPY 2 Google Cloud repository (http://www.ispytrials.org/results/data)
Software and algorithms
stats R package (v.3.6.3)	R Core Team (2020)	https://stat.ethz.ch/R-manual/R-devel/library/stats/html/stats-package.html
lmtest R package (v.0.937)	Zeileis et al., 200252	https://CRAN.R-project.org/package=lmtest
googleVis R package (v.0.6.4)	Gesmann and de Castillo, 201153	https://CRAN.R-project.org/package=googleVis
survival R package (v.3.1–12)	Therneau et al., 200054	https://CRAN.R-project.org/package=survival
forestplot R package (version 2.0.1)	Max Gordon	https://CRAN.R-project.org/package=forestplot