This repository contains the scripts, meta data metrics files used in the manuscript: Archival single cell sequencing reveals persistent subclones over years to decades of DCIS progression.
R scripts in this directory includes all of the codes that could reproduce figures of Arc-well paper.
- snakemake_files: includes the workflow of downsampling coverage calculations
- CNA_pipeline: includes the workflow of initial QC and variable binning, prepares the inputs for downstream analysis, can be found here.
data required for the R scripts under scripts folder
includes filtering files, QC metrics, clinical, computational meta data from cell lines, FFPE samples.
R scripts are dependent on CopyKit(v0.1.0), which can be installed by:
devtools::install_github(repo = "navinlabcode/copykit",ref="f709a48")Session info:
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] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 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
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.54.0 ggthemes_4.2.4 prabclus_2.3-2
[5] bit64_4.0.5 knitr_1.37 DelayedArray_0.20.0 data.table_1.14.2
[9] KEGGREST_1.34.0 RCurl_1.98-1.6 doParallel_1.0.17 generics_0.1.2
[13] RSQLite_2.2.10 bit_4.0.4 tzdb_0.2.0 httpuv_1.6.5
[17] xml2_1.3.3 lubridate_1.8.0 assertthat_0.2.1 viridis_0.6.2
[21] amap_0.8-18 xfun_0.30 hms_1.1.1 promises_1.2.0.1
[25] DEoptimR_1.0-10 fansi_1.0.2 restfulr_0.0.13 progress_1.2.2
[29] dbplyr_2.1.1 readxl_1.3.1 igraph_1.2.11 DBI_1.1.2
[33] geneplotter_1.72.0 tmvnsim_1.0-2 reshape_0.8.8 ellipsis_0.3.2
[37] ggnewscale_0.4.6 backports_1.4.1 annotate_1.72.0 biomaRt_2.50.3
[41] ggalluvial_0.12.3 vctrs_0.3.8 abind_1.4-5 cachem_1.0.6
[45] withr_2.4.3 robustbase_0.93-9 lasso2_1.2-22 GenomicAlignments_1.30.0
[49] treeio_1.18.1 prettyunits_1.1.1 mclust_5.4.9 mnormt_2.0.2
[53] cluster_2.1.2 segmented_1.4-0 lazyeval_0.2.2 crayon_1.5.0
[57] genefilter_1.76.0 edgeR_3.36.0 pkgconfig_2.0.3 nlme_3.1-155
[61] vipor_0.4.5 nnet_7.3-17 pals_1.7 diptest_0.76-0
[65] rlang_1.0.1 miniUI_0.1.1.1 lifecycle_1.0.1 filelock_1.0.2
[69] extrafontdb_1.0 BiocFileCache_2.2.1 modelr_0.1.8 dichromat_2.0-0
[73] ggrastr_1.0.1 cellranger_1.1.0 graph_1.72.0 Matrix_1.4-0
[77] aplot_0.1.2 carData_3.0-5 reprex_2.0.1 beeswarm_0.4.0
[81] GlobalOptions_0.1.2 png_0.1-7 viridisLite_0.4.0 rjson_0.2.21
[85] bitops_1.0-7 ConsensusClusterPlus_1.58.0 KernSmooth_2.23-20 Biostrings_2.62.0
[89] blob_1.2.2 shape_1.4.6 rstatix_0.7.0 gridGraphics_0.5-1
[93] ggsignif_0.6.3 scales_1.1.1 memoise_2.0.1 magrittr_2.0.2
[97] plyr_1.8.6 zlibbioc_1.40.0 compiler_4.1.2 BiocIO_1.4.0
[101] ash_1.0-15 clue_0.3-60 DESeq2_1.34.0 Rsamtools_2.10.0
[105] snakecase_0.11.0 cli_3.2.0 XVector_0.34.0 patchwork_1.1.1
[109] MASS_7.3-55 tidyselect_1.1.2 stringi_1.7.6 proj4_1.0-11
[113] yaml_2.3.5 locfit_1.5-9.4 ggrepel_0.9.1 tools_4.1.2
[117] parallel_4.1.2 rio_0.5.29 circlize_0.4.14 rstudioapi_0.13
[121] bluster_1.4.0 foreach_1.5.2 foreign_0.8-82 logging_0.10-108
[125] janitor_2.1.0 gridExtra_2.3 digest_0.6.29 BiocManager_1.30.16
[129] shiny_1.7.1 fpc_2.2-9 Rcpp_1.0.8.1 car_3.0-11
[133] broom_0.7.12 later_1.3.0 httr_1.4.2 ggdendro_0.1.23
[137] psych_2.1.9 kernlab_0.9-29 colorspace_2.0-3 rvest_1.0.2
[141] XML_3.99-0.9 fs_1.5.2 splines_4.1.2 uwot_0.1.11
[145] yulab.utils_0.0.4 RBGL_1.70.0 tidytree_0.3.8 flexmix_2.3-17
[149] mapproj_1.2.8 ggplotify_0.1.0 xtable_1.8-4 jsonlite_1.8.0
[153] modeltools_0.2-23 ggfun_0.0.5 R6_2.5.1 mime_0.12
[157] htmltools_0.5.2 pillar_1.7.0 glue_1.6.2 fastmap_1.1.0
[161] BiocParallel_1.28.3 BiocNeighbors_1.12.0 class_7.3-20 codetools_0.2-18
[165] maps_3.4.0 utf8_1.2.2 lattice_0.20-45 mixtools_1.2.0
[169] curl_4.3.2 ggbeeswarm_0.6.0 gtools_3.9.2 zip_2.2.0
[173] openxlsx_4.2.5 Rttf2pt1_1.3.10 survival_3.3-0 limma_3.50.1
[177] munsell_0.5.0 GetoptLong_1.0.5 fastcluster_1.2.3 GenomeInfoDbData_1.2.7
[181] iterators_1.0.14 haven_2.4.3 reshape2_1.4.4 gtable_0.3.0
[185] extrafont_0.17
The original sequencing data from this study has been deposited to the Sequence Read Archive (SRA): PRJNA799605.
For any additional information, please email corresponding author.