ecDNA machine learning modeling

1. ecDNA_cargo_gene_modeling_data.csv.gz

The dataset contains features from 386 TCGA tumors for modeling ecDNA cargo gene prediction. It was converted from R data format with the following code. NOTE: columns 'sample' and 'gene_id' are not used for actual modeling but for identifying, and sampling purposes.

library(data.table) data = readRDS("~/../Downloads/ecDNA_cargo_gene_modeling_data.rds") colnames(data)[3] = "total_cn" data.table::fwrite(data, file = "~/../Downloads/ecDNA_cargo_gene_modeling_data.csv.gz", sep = ",")

2. gcap_pcawg_WGS_result.tar.gz

GCAP analysis results for PCAWG allele-specific copy number profiles derived from WGS.

3. gcap_tcga_snp6_result.tar.gz

GCAP analysis results for TCGA allele-specific copy number profiles derived from SNP6 array.

4. gcap_Changkang_WES_result.tar.gz

GCAP analysis results for SYSUCC Changkang allele-specific copy number profiles derived from tumor-normal paired WES.

5. tcga_overlap_gene_wgs.rds, tcga_overlap_gene_snp.rds and tcga_overlap_gene_wes.rds

These datasets contain TCGA gene-level copy number results in R data format from overlapping samples (dataset above). WGS from PCAWG, SNP array, and WES from GDC portal.

6. cellline-batch1.zip & cellline-batch1.zip

GCAP results of cell line batch 1 and batch 2.

7. AA_cellline_wgs.zip

AA software results for cell line batch 1.

8. Batch2_AA_summary.xlsx

AA software results for cell line batch 2.

9. FISH-for-supp-file.zip

Extended raw FISH images from 12 CRC samples.

10. SNU216.zip

Extended AA and GCAP analysis on SNU216.

11. aa_ffpe.zip and AA_summary_table_of_6_erbb2_ffpe_samples.xlsx

Extended AA running files (all results) and result summary data for 6 GCAP predicted ERBB2 amp clinical samples.

12. source data of fig.4

13. source data of supp fig.2 subplots