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 24.04.2 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_2.24.0 class_7.3-23
## [5] pRoloc_1.48.0 BiocParallel_1.42.0
## [7] MLInterfaces_1.88.1 cluster_2.1.8.1
## [9] annotate_1.86.0 XML_3.99-0.18
## [11] AnnotationDbi_1.70.0 bioDist_1.80.0
## [13] KernSmooth_2.23-26 factoextra_1.0.7
## [15] pRolocdata_1.46.0 MSnbase_2.34.1
## [17] ProtGenerics_1.40.0 mzR_2.42.0
## [19] Rcpp_1.1.0 QFeatures_1.19.1
## [21] MultiAssayExperiment_1.34.0 BSgenome.Dmelanogaster.UCSC.dm2_1.4.0
## [23] BSgenome_1.76.0 rtracklayer_1.68.0
## [25] BiocIO_1.18.0 Biostrings_2.76.0
## [27] XVector_0.48.0 rWSBIM1207_0.1.19
## [29] airway_1.28.0 SummarizedExperiment_1.38.1
## [31] Biobase_2.68.0 GenomicRanges_1.60.0
## [33] GenomeInfoDb_1.44.0 IRanges_2.42.0
## [35] S4Vectors_0.46.0 BiocGenerics_0.54.0
## [37] generics_0.1.4 MatrixGenerics_1.20.0
## [39] matrixStats_1.5.0 BiocStyle_2.36.0
## [41] lattice_0.22-6 patchwork_1.3.0
## [43] ggbeeswarm_0.7.2 plotly_4.10.4
## [45] Hmisc_5.2-3 lubridate_1.9.4
## [47] forcats_1.0.0 stringr_1.5.1
## [49] dplyr_1.1.4 purrr_1.0.4
## [51] readr_2.1.5 tidyr_1.3.1
## [53] tibble_3.2.1 ggplot2_3.5.2
## [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_1.2.5
## [10] R6_2.6.1 lazyeval_0.2.2 mgcv_1.9-1
## [13] GetoptLong_1.0.5 withr_3.0.2 prettyunits_1.2.0
## [16] gridExtra_2.3 preprocessCore_1.70.0 cli_3.6.5
## [19] Cairo_1.6-2 isoband_0.2.7 labeling_0.4.3
## [22] sass_0.4.10 mvtnorm_1.3-3 randomForest_4.7-1.2
## [25] proxy_0.4-27 Rsamtools_2.24.0 foreign_0.8-90
## [28] parallelly_1.44.0 MetaboCoreUtils_1.16.1 plotrix_3.8-4
## [31] limma_3.64.1 rstudioapi_0.17.1 impute_1.82.0
## [34] RSQLite_2.3.11 FNN_1.1.4.1 shape_1.4.6.1
## [37] vroom_1.6.5 gtools_3.9.5 car_3.1-3
## [40] dendextend_1.19.0 Matrix_1.7-3 MALDIquant_1.22.3
## [43] abind_1.4-8 lifecycle_1.0.4 yaml_2.3.10
## [46] carData_3.0-5 recipes_1.3.1 SparseArray_1.8.0
## [49] BiocFileCache_2.16.0 blob_1.2.4 crayon_1.5.3
## [52] PSMatch_1.13.2 KEGGREST_1.48.0 magick_2.8.6
## [55] pillar_1.10.2 knitr_1.50 rjson_0.2.23
## [58] lpSolve_5.6.23 future.apply_1.11.3 codetools_0.2-20
## [61] glue_1.8.0 pcaMethods_2.0.0 data.table_1.17.4
## [64] vctrs_0.6.5 png_0.1-8 gtable_0.3.6
## [67] kernlab_0.9-33 cachem_1.1.0 gower_1.0.2
## [70] xfun_0.52 prodlim_2025.04.28 S4Arrays_1.8.0
## [73] coda_0.19-4.1 survival_3.8-3 ncdf4_1.24
## [76] timeDate_4041.110 iterators_1.0.14 hardhat_1.4.1
## [79] lava_1.8.1 statmod_1.5.0 ipred_0.9-15
## [82] nlme_3.1-168 bit64_4.6.0-1 progress_1.2.3
## [85] filelock_1.0.3 LaplacesDemon_16.1.6 bslib_0.9.0
## [88] affyio_1.78.0 vipor_0.4.7 rpart_4.1.24
## [91] colorspace_2.1-1 DBI_1.2.3 nnet_7.3-20
## [94] tidyselect_1.2.1 bit_4.6.0 compiler_4.5.0
## [97] curl_6.2.3 graph_1.86.0 httr2_1.1.2
## [100] htmlTable_2.4.3
## [ 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", "GenomeInfoDb", "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", "stats", "stats4", "stringr",
"SummarizedExperiment", "tibble", "tidyr", "tidyverse", "UpSetR",
"utils", "Vennerable", "XML", "XVector")Page built: 2025-07-22 using R version 4.5.0 (2025-04-11)