{"id":19434409,"url":"https://github.com/likelet/scrcgenomics","last_synced_at":"2026-06-06T23:32:37.248Z","repository":{"id":180579905,"uuid":"663387938","full_name":"likelet/SCRCgenomics","owner":"likelet","description":"Sourcecode for SCRC 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SCRCgenomics\nSourcecode for SCRC project.\n\n# R session info \n\n``` r\nsessioninfo::session_info()\n─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────\nsetting  value\nversion  R version 4.2.1 (2022-06-23)\n os       Ubuntu 20.04.6 LTS\n system   x86_64, linux-gnu\n ui       RStudio\n language (EN)\n collate  en_US.UTF-8\n ctype    en_US.UTF-8\n tz       Etc/UTC\n date     2023-07-08\n rstudio  2022.07.2+576 Spotted Wakerobin (server)\n pandoc   2.19.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)\n\n─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────\n package                     * version   date (UTC) lib source\n abind                         1.4-5     2016-07-21 [1] RSPM (R 4.2.0)\n assertthat                    0.2.1     2019-03-21 [1] RSPM (R 4.2.0)\n backports                     1.4.1     2021-12-13 [1] RSPM (R 4.2.0)\n Biobase                     * 2.58.0    2022-11-01 [1] Bioconductor\n BiocGenerics                * 0.44.0    2022-11-01 [1] Bioconductor\n BiocIO                        1.8.0     2022-11-01 [1] Bioconductor\n BiocParallel                  1.32.6    2023-03-17 [1] Bioconductor\n Biostrings                  * 2.66.0    2022-11-01 [1] Bioconductor\n bitops                        1.0-7     2021-04-24 [1] RSPM (R 4.2.0)\n boot                          1.3-28    2021-05-03 [4] CRAN (R 4.2.1)\n broom                         1.0.1     2022-08-29 [1] RSPM (R 4.2.0)\n broom.helpers                 1.9.0     2022-09-23 [1] RSPM (R 4.2.0)\n BSgenome                    * 1.66.3    2023-02-16 [1] Bioconductor\n BSgenome.Hsapiens.UCSC.hg19 * 1.4.3     2023-05-09 [1] Bioconductor\n car                           3.1-1     2022-10-19 [1] RSPM (R 4.2.0)\n carData                       3.0-5     2022-01-06 [1] RSPM (R 4.2.0)\n circlize                      0.4.15    2022-05-10 [1] RSPM (R 4.2.0)\n cli                           3.4.1     2022-09-23 [1] RSPM (R 4.2.0)\n clue                          0.3-62    2022-10-18 [1] RSPM (R 4.2.0)\n cluster                     * 2.1.3     2022-03-28 [4] CRAN (R 4.2.1)\n codetools                     0.2-18    2020-11-04 [4] CRAN (R 4.2.1)\n colorspace                    2.0-3     2022-02-21 [1] RSPM (R 4.2.0)\n ComplexHeatmap              * 2.14.0    2022-11-01 [1] Bioconductor\n cowplot                     * 1.1.1     2020-12-30 [1] RSPM (R 4.2.0)\n crayon                        1.5.2     2022-09-29 [1] RSPM (R 4.2.0)\n data.table                  * 1.14.4    2022-10-17 [1] RSPM (R 4.2.0)\n DBI                           1.1.3     2022-06-18 [1] RSPM (R 4.2.0)\n DelayedArray                  0.24.0    2022-11-01 [1] Bioconductor\n digest                        0.6.30    2022-10-18 [1] RSPM (R 4.2.0)\n doParallel                  * 1.0.17    2022-02-07 [1] RSPM (R 4.2.0)\n dplyr                       * 1.0.10    2022-09-01 [1] RSPM (R 4.2.0)\n ellipsis                      0.3.2     2021-04-29 [1] RSPM (R 4.2.0)\n evaluate                      0.17      2022-10-07 [1] RSPM (R 4.2.0)\n fansi                         1.0.3     2022-03-24 [1] RSPM (R 4.2.0)\n fastmap                       1.1.0     2021-01-25 [1] RSPM (R 4.2.0)\n finalfit                    * 1.0.5     2022-08-09 [1] RSPM (R 4.2.0)\n forcats                       0.5.2     2022-08-19 [1] RSPM (R 4.2.0)\n foreach                     * 1.5.2     2022-02-02 [1] RSPM (R 4.2.0)\n formatR                       1.12      2022-03-31 [1] RSPM (R 4.2.0)\n Formula                       1.2-4     2020-10-16 [1] RSPM (R 4.2.0)\n futile.logger               * 1.4.3     2016-07-10 [1] RSPM (R 4.2.0)\n futile.options                1.0.1     2018-04-20 [1] RSPM (R 4.2.0)\n generics                      0.1.3     2022-07-05 [1] RSPM (R 4.2.0)\n GenomeInfoDb                * 1.34.9    2023-02-02 [1] Bioconductor\n GenomeInfoDbData              1.2.9     2023-05-16 [1] Bioconductor\n GenomicAlignments             1.34.1    2023-03-09 [1] Bioconductor\n GenomicRanges               * 1.50.2    2022-12-16 [1] Bioconductor\n GetoptLong                    1.0.5     2020-12-15 [1] RSPM (R 4.0.3)\n gg.gap                      * 1.3       2019-09-30 [1] RSPM (R 4.0.0)\n ggalluvial                    0.12.3    2020-12-05 [1] RSPM (R 4.0.3)\n ggplot2                     * 3.3.6     2022-05-03 [1] RSPM (R 4.2.0)\n ggpubr                      * 0.4.0     2020-06-27 [1] RSPM (R 4.2.0)\n ggrepel                     * 0.9.1     2021-01-15 [1] RSPM (R 4.2.0)\n ggsci                       * 2.9       2018-05-14 [1] RSPM (R 4.2.0)\n ggsignif                      0.6.4     2022-10-13 [1] RSPM (R 4.2.0)\n ggthemr                     * 1.1.0     2021-12-14 [2] Github (cttobin/ggthemr@4a31e0d)\n GlobalOptions                 0.1.2     2020-06-10 [1] RSPM (R 4.0.3)\n glue                          1.6.2     2022-02-24 [1] RSPM (R 4.2.0)\n gridBase                      0.4-7     2014-02-24 [1] RSPM (R 4.0.3)\n gridExtra                   * 2.3       2017-09-09 [1] RSPM (R 4.2.0)\n gt                            0.7.0     2022-08-25 [1] RSPM (R 4.2.0)\n gtable                        0.3.1     2022-09-01 [1] RSPM (R 4.2.0)\n gtsummary                   * 1.6.2     2022-09-30 [1] RSPM (R 4.2.0)\n hms                           1.1.2     2022-08-19 [1] RSPM (R 4.2.0)\n htmltools                   * 0.5.3     2022-07-18 [1] RSPM (R 4.2.0)\n httr                          1.4.4     2022-08-17 [1] RSPM (R 4.2.0)\n IRanges                     * 2.32.0    2022-11-01 [1] Bioconductor\n iterators                   * 1.0.14    2022-02-05 [1] RSPM (R 4.2.0)\n kableExtra                    1.3.4     2021-02-20 [1] RSPM (R 4.2.0)\n km.ci                         0.5-2     2009-08-30 [2] RSPM (R 4.0.3)\n KMsurv                        0.1-5     2012-12-03 [2] RSPM (R 4.0.3)\n knitr                         1.40      2022-08-24 [1] RSPM (R 4.2.0)\n lambda.r                      1.2.4     2019-09-18 [1] RSPM (R 4.2.0)\n lattice                     * 0.20-45   2021-09-22 [4] CRAN (R 4.2.1)\n lifecycle                     1.0.3     2022-10-07 [1] RSPM (R 4.2.0)\n lpSolve                       5.6.17    2022-10-10 [1] RSPM (R 4.2.0)\n maftools                    * 2.6.05    2021-02-04 [2] Bioconductor\n magrittr                    * 2.0.3     2022-03-30 [1] RSPM (R 4.2.0)\n MASS                          7.3-57    2022-04-22 [4] CRAN (R 4.2.1)\n Matrix                        1.5-1     2022-09-13 [1] RSPM (R 4.2.0)\n MatrixGenerics                1.10.0    2022-11-01 [1] Bioconductor\n matrixStats                   0.62.0    2022-04-19 [1] RSPM (R 4.2.0)\n mice                          3.14.0    2021-11-24 [1] RSPM (R 4.2.0)\n munsell                       0.5.0     2018-06-12 [1] RSPM (R 4.2.0)\n MutationalPatterns          * 3.8.1     2023-01-26 [3] Bioconductor\n neutralitytestr             * 0.0.3     2021-02-16 [1] RSPM (R 4.0.3)\n NMF                         * 0.24.0    2022-03-29 [1] RSPM (R 4.2.1)\n pheatmap                    * 1.0.12    2019-01-04 [1] RSPM (R 4.2.0)\n pillar                        1.8.1     2022-08-19 [1] RSPM (R 4.2.0)\n pkgconfig                     2.0.3     2019-09-22 [1] RSPM (R 4.2.0)\n pkgmaker                    * 0.32.2    2020-10-20 [1] RSPM (R 4.0.3)\n plyr                        * 1.8.7     2022-03-24 [1] RSPM (R 4.2.0)\n png                           0.1-7     2013-12-03 [1] RSPM (R 4.2.0)\n pracma                        2.4.2     2022-09-22 [1] RSPM (R 4.2.0)\n purrr                         0.3.5     2022-10-06 [1] RSPM (R 4.2.0)\n R6                            2.5.1     2021-08-19 [1] RSPM (R 4.2.0)\n RColorBrewer                * 1.1-3     2022-04-03 [1] RSPM (R 4.2.0)\n Rcpp                          1.0.9     2022-07-08 [1] RSPM (R 4.2.0)\n RCurl                         1.98-1.9  2022-10-03 [1] RSPM (R 4.2.0)\n readr                         2.1.3     2022-10-01 [1] RSPM (R 4.2.0)\n registry                    * 0.5-1     2019-03-05 [1] RSPM (R 4.0.0)\n reshape2                    * 1.4.4     2020-04-09 [1] RSPM (R 4.2.0)\n restfulr                      0.0.15    2022-06-16 [1] RSPM (R 4.2.1)\n rjson                         0.2.21    2022-01-09 [1] RSPM (R 4.2.0)\n rlang                         1.0.6     2022-09-24 [1] RSPM (R 4.2.0)\n rmarkdown                     2.17      2022-10-07 [1] RSPM (R 4.2.0)\n Rmisc                       * 1.5.1     2022-05-02 [1] RSPM (R 4.2.0)\n rngtools                    * 1.5.2     2021-09-20 [1] RSPM (R 4.2.0)\n Rsamtools                     2.14.0    2022-11-01 [1] Bioconductor\n rstatix                       0.7.0     2021-02-13 [1] RSPM (R 4.2.0)\n rstudioapi                    0.14      2022-08-22 [1] RSPM (R 4.2.0)\n rtracklayer                 * 1.58.0    2022-11-01 [1] Bioconductor\n rvest                         1.0.3     2022-08-19 [1] RSPM (R 4.2.0)\n S4Vectors                   * 0.36.2    2023-02-26 [1] Bioconductor\n sampling                    * 2.9       2021-01-13 [1] RSPM (R 4.0.3)\n scales                      * 1.2.1     2022-08-20 [1] RSPM (R 4.2.0)\n sessioninfo                   1.2.2     2021-12-06 [1] RSPM (R 4.2.0)\n shape                         1.4.6     2021-05-19 [1] RSPM (R 4.2.0)\n stringi                       1.7.8     2022-07-11 [1] RSPM (R 4.2.0)\n stringr                       1.4.1     2022-08-20 [1] RSPM (R 4.2.0)\n SummarizedExperiment          1.28.0    2022-11-01 [1] Bioconductor\n survival                    * 3.3-1     2022-03-03 [4] CRAN (R 4.2.1)\n survminer                   * 0.4.9     2021-03-09 [2] RSPM (R 4.0.3)\n survMisc                      0.5.5     2018-07-05 [2] RSPM (R 4.0.3)\n svglite                       2.0.0     2021-02-20 [2] RSPM (R 4.0.4)\n systemfonts                   1.0.4     2022-02-11 [1] RSPM (R 4.2.0)\n table1                      * 1.4.2     2021-06-06 [1] RSPM (R 4.2.0)\n tibble                        3.1.8     2022-07-22 [1] RSPM (R 4.2.0)\n tidyr                       * 1.2.1     2022-09-08 [1] RSPM (R 4.2.0)\n tidyselect                    1.2.0     2022-10-10 [1] RSPM (R 4.2.0)\n tzdb                          0.3.0     2022-03-28 [1] RSPM (R 4.2.0)\n utf8                          1.2.2     2021-07-24 [1] RSPM (R 4.2.0)\n vctrs                         0.5.0     2022-10-22 [1] RSPM (R 4.2.0)\n VennDiagram                 * 1.6.20    2018-03-28 [2] RSPM (R 4.0.0)\n viridisLite                   0.4.1     2022-08-22 [1] RSPM (R 4.2.0)\n webshot                       0.5.2     2019-11-22 [2] RSPM (R 4.0.3)\n wesanderson                 * 0.3.6     2018-04-20 [1] RSPM (R 4.0.0)\n withr                         2.5.0     2022-03-03 [1] RSPM (R 4.2.0)\n xfun                          0.34      2022-10-18 [1] RSPM (R 4.2.0)\n XML                           3.99-0.11 2022-10-03 [1] RSPM (R 4.2.0)\n xml2                          1.3.3     2021-11-30 [1] RSPM (R 4.2.0)\n xtable                        1.8-4     2019-04-21 [1] RSPM (R 4.2.0)\n XVector                     * 0.38.0    2022-11-01 [1] Bioconductor\n yaml                          2.3.6     2022-10-18 [1] RSPM (R 4.2.0)\n zlibbioc                      1.44.0    2022-11-01 [1] Bioconductor\n zoo                           1.8-11    2022-09-17 [1] RSPM (R 4.2.0)\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Fscrcgenomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flikelet%2Fscrcgenomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Fscrcgenomics/lists"}