The following packages have been used to generate this document.
## R version 4.5.0 (2025-04-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /opt/R-4.5/lib/R/lib/libRblas.so
## LAPACK: /opt/R-4.5/lib/R/lib/libRlapack.so; LAPACK version 3.12.1
##
## 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] grid stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] UpSetR_1.4.0 Vennerable_3.1.0.9000
## [3] ComplexHeatmap_2.26.0 class_7.3-23
## [5] pRoloc_1.50.0 BiocParallel_1.44.0
## [7] MLInterfaces_1.90.0 cluster_2.1.8.1
## [9] annotate_1.88.0 XML_3.99-0.20
## [11] AnnotationDbi_1.72.0 bioDist_1.82.0
## [13] KernSmooth_2.23-26 factoextra_1.0.7
## [15] pRolocdata_1.48.0 MSnbase_2.36.0
## [17] ProtGenerics_1.42.0 mzR_2.44.0
## [19] Rcpp_1.1.0 QFeatures_1.20.0
## [21] MultiAssayExperiment_1.36.1 BSgenome.Dmelanogaster.UCSC.dm2_1.4.0
## [23] BSgenome_1.78.0 rtracklayer_1.70.1
## [25] BiocIO_1.20.0 Biostrings_2.78.0
## [27] XVector_0.50.0 rWSBIM1207_0.1.19
## [29] airway_1.30.0 SummarizedExperiment_1.40.0
## [31] Biobase_2.70.0 GenomicRanges_1.62.1
## [33] Seqinfo_1.0.0 IRanges_2.44.0
## [35] S4Vectors_0.48.0 BiocGenerics_0.56.0
## [37] generics_0.1.4 MatrixGenerics_1.22.0
## [39] matrixStats_1.5.0 BiocStyle_2.38.0
## [41] lattice_0.22-7 patchwork_1.3.2
## [43] ggbeeswarm_0.7.3 plotly_4.11.0
## [45] Hmisc_5.2-5 lubridate_1.9.4
## [47] forcats_1.0.1 stringr_1.6.0
## [49] dplyr_1.1.4 purrr_1.2.0
## [51] readr_2.1.6 tidyr_1.3.1
## [53] tibble_3.3.0 ggplot2_4.0.1
## [55] tidyverse_2.0.0 rWSBIM1322_0.3.2
##
## loaded via a namespace (and not attached):
## [1] segmented_2.1-4 fs_1.6.6 bitops_1.0-9
## [4] httr_1.4.7 RColorBrewer_1.1-3 doParallel_1.0.17
## [7] tools_4.5.0 backports_1.5.0 utf8_1.2.6
## [10] R6_2.6.1 lazyeval_0.2.2 mgcv_1.9-4
## [13] GetoptLong_1.1.0 withr_3.0.2 prettyunits_1.2.0
## [16] gridExtra_2.3 preprocessCore_1.72.0 cli_3.6.5
## [19] Cairo_1.7-0 isoband_0.3.0 labeling_0.4.3
## [22] sass_0.4.10 mvtnorm_1.3-3 S7_0.2.1
## [25] randomForest_4.7-1.2 proxy_0.4-28 Rsamtools_2.26.0
## [28] foreign_0.8-90 parallelly_1.46.0 MetaboCoreUtils_1.18.1
## [31] plotrix_3.8-13 limma_3.66.0 rstudioapi_0.17.1
## [34] impute_1.84.0 RSQLite_2.4.5 FNN_1.1.4.1
## [37] shape_1.4.6.1 vroom_1.6.7 gtools_3.9.5
## [40] car_3.1-3 dendextend_1.19.1 Matrix_1.7-4
## [43] MALDIquant_1.22.3 abind_1.4-8 lifecycle_1.0.4
## [46] yaml_2.3.12 carData_3.0-5 recipes_1.3.1
## [49] SparseArray_1.10.7 BiocFileCache_3.0.0 blob_1.2.4
## [52] crayon_1.5.3 PSMatch_1.14.0 cigarillo_1.0.0
## [55] KEGGREST_1.50.0 pillar_1.11.1 knitr_1.50
## [58] rjson_0.2.23 lpSolve_5.6.23 future.apply_1.20.1
## [61] codetools_0.2-20 glue_1.8.0 pcaMethods_2.2.0
## [64] data.table_1.17.8 vctrs_0.6.5 png_0.1-8
## [67] gtable_0.3.6 kernlab_0.9-33 cachem_1.1.0
## [70] gower_1.0.2 xfun_0.55 prodlim_2025.04.28
## [73] S4Arrays_1.10.1 coda_0.19-4.1 survival_3.8-3
## [76] ncdf4_1.24 timeDate_4051.111 iterators_1.0.14
## [79] hardhat_1.4.2 lava_1.8.2 statmod_1.5.1
## [82] ipred_0.9-15 nlme_3.1-168 bit64_4.6.0-1
## [85] progress_1.2.3 filelock_1.0.3 LaplacesDemon_16.1.6
## [88] bslib_0.9.0 affyio_1.80.0 vipor_0.4.7
## [91] otel_0.2.0 rpart_4.1.24 colorspace_2.1-2
## [94] DBI_1.2.3 nnet_7.3-20 tidyselect_1.2.1
## [97] bit_4.6.0 compiler_4.5.0 curl_7.0.0
## [100] graph_1.88.1
## [ reached 'max' / getOption("max.print") -- omitted 72 entries ]To install all necessary packages to run all the code, please execute the following code:
pkgs <- c("airway", "annotate", "AnnotationDbi", "base", "Biobase",
"BiocGenerics", "BiocIO", "BiocParallel", "BiocStyle", "bioDist",
"Biostrings", "BSgenome.Dmelanogaster.UCSC.dm2", "BSgenome", "class",
"cluster", "ComplexHeatmap", "datasets", "dplyr", "factoextra",
"forcats", "generics", "GenomicRanges", "ggbeeswarm", "ggplot2",
"graphics", "grDevices", "grid", "Hmisc", "IRanges", "KernSmooth",
"lattice", "lubridate", "MatrixGenerics", "matrixStats", "methods",
"MLInterfaces", "MSnbase", "MultiAssayExperiment", "mzR", "patchwork",
"plotly", "pRoloc", "pRolocdata", "ProtGenerics", "purrr", "QFeatures",
"Rcpp", "readr", "rtracklayer", "rWSBIM1207", "rWSBIM1322",
"S4Vectors", "Seqinfo", "stats", "stats4", "stringr",
"SummarizedExperiment", "tibble", "tidyr", "tidyverse", "UpSetR",
"utils", "Vennerable", "XML", "XVector")Page built: 2026-01-12 using R version 4.5.0 (2025-04-11)