labsyspharm/cd73_coy_spatialcorrelation: Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma - Figure scripts

For an example of the spatial correlation calculation for Tumor CD73 expression and Monocyte CD39 expression, download CD73NatComm_Coy2021_CyCIF_TMAdata.mat from https://www.synapse.org/#!Synapse:syn31840602 and run example_spatcorr.m in MATLAB. Runtime should be within a couple minutes.

corr_knn2.m is the core function for computing spatial correlations using the kNN algorithm and Pearson correlations.

subpop_spatcorr_express.m and subpop_spatcorr_express_self.m compute a given spatial correlation relation for all the TMA cores, perform exponential fitting, and evaluate statistical significance.

all_spatcorrs.m and all_spatcorrs2.m compute all the different spatial correlations (e.g. between different populations and/or expression levels) that were considered in this study. 

This code has been tested on a MATLAB v2018a on a Windows 10 OS. 

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Similar spatial correlation analyses were repeated on CHOP TMA data, which can be found in CD73NatComm_Coy2021_CyCIF_CHOPTMAdata.mat from https://www.synapse.org/#!Synapse:syn31840603.

CHOPTMA_spatcorrs.m computes all the spatial correlations on the CHOP TMA subsequently considered in this study.

CHOPTMArnaproteincycif.m plots comparisons of the average CD73 and CD39 intensities measured by CyCIF relative to protein or RNA measurements made on the same CHOP specimens.

CHOPTMA_figures.m plots the spatial correlations of CHOP TMA cores that were not from control specimens. 

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TCGA_GBM_immune_analysis.html includes TCGA bulk full-length RNA-seq data analysis of GBM for the manuscript "Single Cell Spatial Analysis Reveals the Topology of Immunomodulatory Purinergic Signaling in Glioblastoma".

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cycif-msi.py was used to generate a datatable from https://www.synapse.org/#!Synapse:syn30804043 for comparing CyCIF and MSI results. The required python packages are listed in requirements_cycif_msi.txt . 

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KMcurve_fig.m is used to generate survival curves from CD73NatComm_Coy2021_CyCIF_TMAdata.mat .
subtype_comp_fig.m generates boxplot figures of a few gross cell-types from CD73NatComm_Coy2021_CyCIF_TMAdata.mat .