REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-FoxP3 antibody; clone SP97	Spring Biosciences	RRID: AB_10658507
Anti-pan-cytokeratin; clone AE1/AE3	Dako	RRID: AB_2631307
Anti-CD20; clone L26	Ventana/Roche	RRID: AB_2335956
Anti-CD3; clone 2GV6	Ventana/Roche	RRID: AB_2335978
Anti-Ki67; clone 30-9	Ventana/Roche	RRID: AB_2631262
Anti-CD117; clone D3W6Y	Cell Signaling	RRID: AB_2799120
Anti-PD-L1; clone E1L3N	Cell Signaling	RRID: AB_2687655
Anti-PD-1; clone EPR4877	Abcam	RRID: AB_2894867
Anti-CD8; clone 4B11	Leica	RRID: AB_442068
Anti-CD68; clone PG-M1	Dako	RRID: AB_2074844
Biological samples
Tumor biopsy before treatment	I-SPY 2 trial	https://clinicaltrials.gov/ct2/show/NCT01042379
Critical commercial assays
Custom Agilent 44K expression arrays	Agendia, Inc	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20078 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL30483
MammaPrint	Agendia, Inc	https://agendia.com/mammaprint/
BluePrint	Agendia, Inc	https://agendia.com/blueprint/
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 transcriptomic data	GEO accession number	Gene Expression Omnibus (GEO) SubSeries GSE194040 (mRNA), (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194040), within the SuperSeries GSE196096 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196096)
Raw RPPA data	GEO accession number	Gene Expression Omnibus (GEO) SubSeries GSE196093 (RPPA) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196093), within the SuperSeries GSE196096 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196096).
Patient-level mIF features	This study	https://www.ispytrials.org/results/data
Patient-level expression signature scores	This study	https://www.ispytrials.org/results/data
Patient-level RPPA markers	This study	https://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.0.9–37)	Zeileis A, Hothorn T (2002). “Diagnostic Checking in Regression Relationships.” R News, 2(3), 7–10.	https://CRAN.R-project.org/package=lmtest
rjags R package (v.4-10)	Martyn Plummer (2019). rjags: Bayesian Graphical Models using MCMC. R package v4-10.	https://CRAN.R-project.org/package=rjags
phenoptr R package	Johnson K (2022). phenoptr: inForm Helper Functions. R package version 0.3.2	https://akoyabio.github.io/phenoptr/
spatstat R package	A. Baddeley, E. Rubak and R.Turner. Spatial Point Patterns: Methodology and Applications with R. Chapman and Hall/CRC Press, 2015.	https://spatstat.org/
divo R package	Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Cankun Wang, Grzegorz Rempala (2019)	https://CRAN.R-project.org/package=divo
R scripts	N/A	Zenodo: https://doi.org/10.5281/zenodo.13323763