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Data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA" - MaRDI portal

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Data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA"

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DOI10.5281/zenodo.10829212Zenodo10829212MaRDI QIDQ6725796

Dataset published at Zenodo repository.

Author name not available (Why is that?)

Publication date: 18 March 2024

Copyright license: No records found.



Description

This submission has processed data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA". The `data` folder contains processed information for the Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) datasets. The HPA data is found in `data/hpa` and contains gene ranks used to compute the thymus-likeness score (TLS) and files where the TLS has been calculated for the HPA tissues. The TCGA data can be found in `data/proc`, where individual RDS files have been given for each analyzed cohort. These RDS files contain the results of the cutoff scanning procedure mentioned in the manuscript and account for the bulk of the data generated for this study. RDS files can be loaded using the `readRDS` function in an R session. Other information used to create plots is in the `data` folder. The `plots` folder contain the result of plotting the entireity of the cutoff scanning procedure. The manuscript only contains plots for the 28 cohorts where a significant difference in terms of immune difference is observed, and that too, only the final heuristic plots. The `plots/tcga/immuneres` folder has plots at different levels: (i) single cell category/single deconvolution method with permutation tests (ii) single cell category/multiple deconvolution methods and (iii) significant cell categories/representative deconvolution method. Only (iii) is present in the manuscript. Overall, this folder should contain ~2000 plots. The code used to generate this study is deposited at: https://gitlab.com/narencs179/thymus-like-score






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