Codes and data for the manuscript "Mutational signatures are jointly shaped by DNA damage and repair" (Nature Communications 11: 2169 (2020)). R-markdown report is available at https://nvolkova.github.io/signature-interactions/ .
Codes and pre-calculated data to filter and classify mutations in C. elegans data and calculate the contributions of DNA repair and genotoxins to mutational spectra.
Codes for analysing DNA damage-repair interactions in human cancers. Catalogues mutations in DNA repair genes, quantifies selection with dNdS analysis. This part requires a matrix with TCGA variants, and a metadata matrix with sample names, cancer types, and FPKM expression values for DNA repair genes.
Tables with signatures and interaction coefficients for C. elegans analysis, as well as with DNA repair genes and their mutations and selective pressure across TCGA samples.
Compares genotoxin signatures in human cancers (as per COSMIC catalogue) and C. elegans.
Materials for rmarkdown report.
Session information for the analyses:
R version 3.5.1 (2018-07-02)
Matrix products: default
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] deconstructSigs_1.8.0 org.Hs.eg.db_3.7.0 xlsx_0.6.1
[4] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.34.8 AnnotationDbi_1.44.0
[7] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.50.0 rtracklayer_1.42.1
[10] dndscv_0.0.1.0 bayesplot_1.6.0 RColorBrewer_1.1-2
[13] greta_0.2.3 reshape2_1.4.3 ggplot2_3.1.0
[16] VariantAnnotation_1.28.10 Rsamtools_1.34.1 Biostrings_2.50.2
[19] XVector_0.22.0 SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[22] BiocParallel_1.16.5 matrixStats_0.54.0 Biobase_2.42.0
[25] GenomicRanges_1.34.0 GenomeInfoDb_1.18.1 IRanges_2.16.0
[28] S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 lattice_0.20-35 prettyunits_1.0.2
[4] assertthat_0.2.0 digest_0.6.18 R6_2.4.0
[7] plyr_1.8.4 RSQLite_2.1.1 httr_1.4.0
[10] pillar_1.3.1 zlibbioc_1.28.0 rlang_0.3.1
[13] GenomicFeatures_1.34.3 progress_1.2.0 lazyeval_0.2.1
[16] blob_1.1.1 Matrix_1.2-14 stringr_1.3.1
[19] RCurl_1.95-4.11 bit_1.1-14 biomaRt_2.34.2
[22] munsell_0.5.0 compiler_3.5.1 pkgconfig_2.0.2
[25] tidyselect_0.2.5 tibble_2.0.1 GenomeInfoDbData_1.2.0
[28] codetools_0.2-15 XML_3.98-1.16 crayon_1.3.4
[31] dplyr_0.8.0.1 withr_2.1.2 GenomicAlignments_1.18.1
[34] MASS_7.3-50 bitops_1.0-6 grid_3.5.1
[37] gtable_0.2.0 DBI_1.0.0 magrittr_1.5
[40] scales_1.0.0 stringi_1.2.4 seqinr_3.4-5
[43] tools_3.5.1 ade4_1.7-13 bit64_0.9-7
[46] glue_1.3.0 purrr_0.3.0 hms_0.4.2
[49] AnnotationDbi_1.44.0 colorspace_1.4-0 memoise_1.1.0
[52] reticulate_1.11.1 listenv_0.7.0 base64enc_0.1-3
[55] tensorflow_1.10 future_1.12.0 coda_0.19-2
[58] tfruns_1.4 jsonlite_1.6 whisker_0.3-2
[61] globals_0.12.4