Data underlying the PhD thesis: Computational approaches to dissect immunotherapy response in breast cancer

Code underlying the publications described in the thesis. The dataset includes the Python 3, R and bash scripts for bioinformatic analyses included in the following research papers:<br>1) Nederlof, I., Isaeva, O.I., de Graaf, M. <em style="color:rgb(34, 34, 34);">et al.</em> Neoadjuvant nivolumab or nivolumab plus ipilimumab in early-stage triple-negative breast cancer: a phase 2 adaptive trial. <em style="color:rgb(34, 34, 34);">Nat Med</em> <strong style="color:rgb(34, 34, 34);">30</strong>, 3223–3235 (2024). https://doi.org/10.1038/s41591-024-03249-32) Voorwerk, L., Isaeva, O.I., Horlings, H.M. <em style="color:rgb(34, 34, 34);">et al.</em> PD-L1 blockade in combination with carboplatin as immune induction in metastatic lobular breast cancer: the GELATO trial. <em style="color:rgb(34, 34, 34);">Nat Cancer</em> <strong style="color:rgb(34, 34, 34);">4</strong>, 535–549 (2023). https://doi.org/10.1038/s43018-023-00542-x3) Gangaev, A., Ketelaars, S.L.C., Isaeva, O.I. <em style="color:rgb(34, 34, 34);">et al.</em> Identification and characterization of a SARS-CoV-2 specific CD8+ T cell response with immunodominant features. <em style="color:rgb(34, 34, 34);">Nat Commun</em> <strong style="color:rgb(34, 34, 34);">12</strong>, 2593 (2021). https://doi.org/10.1038/s41467-021-22811-y