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

本数据集包含本学位论文中所述各类出版物所依托的代码。本数据集收录了下述研究论文中所涉及的生物信息学分析所用的Python 3、R语言及Bash脚本：
1) Nederlof I、Isaeva O.I、de Graaf M等。早期三阴性乳腺癌新辅助纳武利尤单抗单药或联合伊匹木单抗治疗：一项II期适应性临床试验。《自然·医学（Nat Med）》，2024年，第30卷，3223-3235页。DOI：10.1038/s41591-024-03249-3
2) Voorwerk L、Isaeva O.I、Horlings H.M等。转移性小叶乳腺癌免疫诱导治疗中PD-L1阻断联合卡铂方案：GELATO临床试验。《自然·癌症（Nat Cancer）》，2023年，第4卷，535-549页。DOI：10.1038/s43018-023-00542-x
3) Gangaev A、Ketelaars S.L.C、Isaeva O.I等。具有免疫显性特征的新型冠状病毒（SARS-CoV-2）特异性CD8阳性T细胞应答的鉴定与表征。《自然·通讯（Nat Commun）》，2021年，第12卷，2593页。DOI：10.1038/s41467-021-22811-y