The following packages have been used to generate this document.
## R version 4.3.1 Patched (2023-07-10 r84676)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Manjaro Linux
##
## Matrix products: default
## BLAS: /usr/lib/libblas.so.3.11.0
## LAPACK: /usr/lib/liblapack.so.3.11.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] 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
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Europe/Brussels
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] plotly_4.10.2 factoextra_1.0.7
## [3] gplots_3.1.3 limma_3.56.2
## [5] QFeatures_1.11.1 MultiAssayExperiment_1.26.0
## [7] PSMatch_1.4.0 magrittr_2.0.3
## [9] Spectra_1.10.2 ProtGenerics_1.32.0
## [11] BiocParallel_1.34.2 msigdbr_7.5.1
## [13] clusterProfiler_4.8.2 GO.db_3.17.0
## [15] org.Hs.eg.db_3.17.0 AnnotationDbi_1.62.2
## [17] biomaRt_2.56.1 patchwork_1.1.3
## [19] DESeq2_1.40.2 SummarizedExperiment_1.30.2
## [21] Biobase_2.60.0 MatrixGenerics_1.12.3
## [23] matrixStats_1.0.0 GenomicRanges_1.52.0
## [25] GenomeInfoDb_1.36.1 IRanges_2.34.1
## [27] S4Vectors_0.38.1 BiocGenerics_0.46.0
## [29] DT_0.28 lubridate_1.9.2
## [31] forcats_1.0.0 stringr_1.5.0
## [33] dplyr_1.1.2 purrr_1.0.2
## [35] readr_2.1.4 tidyr_1.3.0
## [37] tibble_3.2.1 tidyverse_2.0.0
## [39] ggplot2_3.4.3 rWSBIM2122_0.4.1
##
## loaded via a namespace (and not attached):
## [1] fs_1.6.3 bitops_1.0-7
## [3] enrichplot_1.20.1 HDO.db_0.99.1
## [5] httr_1.4.7 RColorBrewer_1.1-3
## [7] numDeriv_2016.8-1.1 tools_4.3.1
## [9] backports_1.4.1 utf8_1.2.3
## [11] R6_2.5.1 lazyeval_0.2.2
## [13] apeglm_1.22.1 withr_2.5.0
## [15] prettyunits_1.1.1 gridExtra_2.3
## [17] preprocessCore_1.62.1 cli_3.6.1
## [19] scatterpie_0.2.1 shinyjs_2.1.0
## [21] labeling_0.4.2 sass_0.4.7
## [23] mvtnorm_1.2-3 yulab.utils_0.0.8
## [25] gson_0.1.0 DOSE_3.26.1
## [27] bbmle_1.0.25 rstudioapi_0.15.0
## [29] RSQLite_2.3.1 generics_0.1.3
## [31] gridGraphics_0.5-1 gtools_3.9.4
## [33] crosstalk_1.2.0 vroom_1.6.3
## [35] car_3.1-2 Matrix_1.6-0
## [37] fansi_1.0.4 abind_1.4-5
## [39] lifecycle_1.0.3 yaml_2.3.7
## [41] carData_3.0-5 qvalue_2.32.0
## [43] BiocFileCache_2.8.0 grid_4.3.1
## [45] blob_1.2.4 promises_1.2.1
## [47] crayon_1.5.2 bdsmatrix_1.3-6
## [49] shinydashboard_0.7.2 lattice_0.21-8
## [51] cowplot_1.1.1 mzR_2.34.1
## [53] KEGGREST_1.40.0 pillar_1.9.0
## [55] knitr_1.43 fgsea_1.26.0
## [57] codetools_0.2-19 fastmatch_1.1-4
## [59] glue_1.6.2 downloader_0.4
## [61] ggfun_0.1.2 data.table_1.14.8
## [63] vctrs_0.6.3 png_0.1-8
## [65] treeio_1.24.3 gtable_0.3.4
## [67] emdbook_1.3.13 cachem_1.0.8
## [69] xfun_0.40 S4Arrays_1.0.5
## [71] mime_0.12 tidygraph_1.2.3
## [73] msdata_0.40.0 coda_0.19-4
## [75] ncdf4_1.21 ellipsis_0.3.2
## [77] nlme_3.1-162 ggtree_3.8.2
## [79] bit64_4.0.5 ExploreModelMatrix_1.12.0
## [81] progress_1.2.2 filelock_1.0.2
## [83] bslib_0.5.1 KernSmooth_2.23-22
## [85] colorspace_2.1-0 DBI_1.1.3
## [87] tidyselect_1.2.0 bit_4.0.5
## [89] compiler_4.3.1 curl_5.0.2
## [91] xml2_1.3.5 DelayedArray_0.26.7
## [93] bookdown_0.34.2 shadowtext_0.1.2
## [95] scales_1.2.1 caTools_1.18.2
## [97] rappdirs_0.3.3 digest_0.6.33
## [99] rmarkdown_2.24 XVector_0.40.0
## [ reached getOption("max.print") -- omitted 61 entries ]To install all necessary packages to run all the code, please execute the following code:
pkgs <- c("AnnotationDbi", "base", "Biobase", "BiocGenerics",
"BiocParallel", "biomaRt", "clusterProfiler", "datasets", "DESeq2",
"dplyr", "DT", "factoextra", "forcats", "GenomeInfoDb",
"GenomicRanges", "ggplot2", "GO.db", "gplots", "graphics", "grDevices",
"IRanges", "limma", "lubridate", "magrittr", "MatrixGenerics",
"matrixStats", "methods", "msigdbr", "MultiAssayExperiment",
"org.Hs.eg.db", "patchwork", "plotly", "ProtGenerics", "PSMatch",
"purrr", "QFeatures", "readr", "rWSBIM2122", "S4Vectors", "Spectra",
"stats", "stats4", "stringr", "SummarizedExperiment", "tibble",
"tidyr", "tidyverse", "utils")Page built: 2023-08-28 using R version 4.3.1 Patched (2023-07-10 r84676)