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README.md

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The script figures_run.R contains compiled code from all figures in the paper. In particular,
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- code for training machine learning models that can be used to assess ligand specificity (Figure 1).
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- code for information theoretic frameworks that are employed to quantify the Response Specificity of genes and genesets (Figure 4).
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- code for identifying genes that contribute to a summary metric for Response Specificity, called the Response Specificity Score (Figure 6).
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- code for identifying genes that contribute to a summary metric for Response Specificity, called the Response Specificity Index (Figure 6).
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Intermediate files that are generated as the result of more time-intensive computations are in the folders ./infotheo and ./ml_models.
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Processed scRNAseq data related to Figure 1 (naive macrophages), Figure 5 (polarized macrophages), and Figure 7 (peritoneal macrophages),are provided as .rds files in the folder ./output.

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