This repository contains the metadata, software, and scripts used in the manuscript: Reconstructing mutational lineages in breast cancer by multi-patient-targeted single-cell DNA sequencing.
includes clinical patient information, total genes submitted for multi-patient targeted panel, and bulk exome / single cell sequencing metrics.
R scripts in this directory include all the code required to reproduce the figures in the Mission Bio TNBC paper.
includes Tapestri Insights(v2.2) software, custom panel file, and Tapestri.cnv R Package.
R scripts are dependent on CopyKit(v0.1.0) and Tapestri.cnv, which can be installed by:
devtools::install_github(repo = "navinlabcode/copykit",ref="f709a48")devtools::install_local(path = "tapestri.cnv_0.1.0.tar.gz", repos='http://cran.us.r-project.org', clean = TRUE)Session info:
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] Gini_0.1.0 Rtsne_0.15 ggrepel_0.8.2 magrittr_1.5
[5] tapestri.cnv_1.0.0 hdf5r_1.3.2 BiocParallel_1.18.1 ineq_0.2-13
[9] umap_0.2.6.0 phangorn_2.5.5 ape_5.4-1 circlize_0.4.10
[13] ComplexHeatmap_2.0.0 flowCore_1.50.0 cowplot_1.1.1 forcats_0.5.0
[17] stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4 readr_1.3.1
[21] tidyr_1.1.1 tibble_3.0.3 ggplot2_3.3.2 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] nlme_3.1-148 matrixStats_0.56.0 fs_1.5.0 bit64_4.0.2
[5] lubridate_1.7.9 RColorBrewer_1.1-2 httr_1.4.2 tools_3.6.1
[9] backports_1.1.8 R6_2.4.1 DBI_1.1.0 BiocGenerics_0.30.0
[13] colorspace_1.4-1 GetoptLong_1.0.2 withr_2.2.0 tidyselect_1.1.0
[17] bit_4.0.4 compiler_3.6.1 graph_1.62.0 cli_2.0.2
[21] rvest_0.3.6 Biobase_2.44.0 xml2_1.3.2 scales_1.1.1
[25] DEoptimR_1.0-8 mvtnorm_1.1-1 robustbase_0.93-6 quadprog_1.5-8
[29] askpass_1.1 rrcov_1.5-5 pkgconfig_2.0.3 dbplyr_1.4.4
[33] rlang_0.4.7 GlobalOptions_0.1.2 readxl_1.3.1 rstudioapi_0.11
[37] shape_1.4.4 generics_0.0.2 jsonlite_1.7.0 Matrix_1.2-18
[41] Rcpp_1.0.5 munsell_0.5.0 fansi_0.4.1 reticulate_1.16
[45] lifecycle_0.2.0 stringi_1.4.6 MASS_7.3-52 blob_1.2.1
[49] parallel_3.6.1 crayon_1.3.4 lattice_0.20-41 haven_2.3.1
[53] hms_0.5.3 pillar_1.4.6 igraph_1.2.5 rjson_0.2.20
[57] corpcor_1.6.9 stats4_3.6.1 fastmatch_1.1-0 reprex_0.3.0
[61] glue_1.4.1 modelr_0.1.8 png_0.1-7 vctrs_0.3.2
[65] cellranger_1.1.0 gtable_0.3.0 openssl_1.4.2 clue_0.3-57
[69] assertthat_0.2.1 broom_0.7.0 RSpectra_0.16-0 pcaPP_1.9-73
[73] cluster_2.1.0 ellipsis_0.3.1
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggtree_3.2.1 ape_5.6-2 dendextend_1.15.2
[4] dbscan_1.1-10 copykit_0.1.0 DNAcopy_1.68.0
[7] Rsubread_2.8.1 SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
[10] MatrixGenerics_1.6.0 matrixStats_0.61.0 ggalt_0.4.0
[13] DEGreport_1.33.1 ggpubr_0.4.0 Homo.sapiens_1.3.1
[16] EnsDb.Hsapiens.v86_2.99.0 org.Hs.eg.db_3.14.0 GO.db_3.14.0
[19] OrganismDbi_1.36.0 GenomicFeatures_1.46.5 GenomicRanges_1.46.1
[22] GenomeInfoDb_1.30.1 AnnotationDbi_1.56.2 IRanges_2.28.0
[25] S4Vectors_0.32.3 Biobase_2.54.0 BiocGenerics_0.40.0
[28] RColorBrewer_1.1-2 ComplexHeatmap_2.10.0 forcats_0.5.1
[31] stringr_1.4.0 purrr_0.3.4 readr_2.1.2
[34] tidyverse_1.3.1 tibble_3.1.6 useful_1.2.6
[37] ggplot2_3.3.5 cowplot_1.1.1 tidyr_1.2.0
[40] dplyr_1.0.8
The original sequencing data from this study has been deposited to the Sequence Read Archive (SRA): PRJNA763862, PRJNA629885.
For any additional information, please email corresponding author.