Identification of ovarian high-grade endometrioid-type tumors through multi-omics analysis: JGOG3025-TR2 study

• This page provides codes and data to reproduce the results of the corresponding paper.

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Environment

All codes were tested on MacOS.

Python 3.8.8

• numpuy 1.20.3
• pandas 1.3.4
• scipy 1.7.2
• matplotlib 3.4.3
• scikit-learn 1.0.1
• lifelines 0.26.3
• xbgoost 1.5.1
• umap-learn 0.5.2
• wgbs_tools 0.2.2

R 4.1.2

• sva 3.42.0
• data.table 1.15.0
• DESeq2 1.34.0
• limma 3.50.3
• annotatr 1.20.0
• karyoploteR 1.20.3

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Contents

• data
• code
• download

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Data availability

Genomic data for the JGOG3025-TR2 cohort, including SNP arrays, RNA-seq, and DNA methylation arrays, will be available in the NCBI-GEO with the accsession of GSE263455.
Targeted DNA sequencing and clinical information per sample are available upon reasonable request to Japanese Gynecological Oncology Group (info@jgog.gr.jp, https://jgog.gr.jp/en/index.html)

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Citation

The corresponding paper is under submission.

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