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] 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_2.18.0 class_7.3-22
## [5] pRoloc_1.42.0 BiocParallel_1.36.0
## [7] MLInterfaces_1.82.0 cluster_2.1.4
## [9] annotate_1.80.0 XML_3.99-0.15
## [11] AnnotationDbi_1.64.1 bioDist_1.74.0
## [13] KernSmooth_2.23-22 factoextra_1.0.7
## [15] pRolocdata_1.40.0 MSnbase_2.28.1
## [17] ProtGenerics_1.34.0 mzR_2.36.0
## [19] Rcpp_1.0.11 QFeatures_1.12.0
## [21] MultiAssayExperiment_1.28.0 BSgenome.Dmelanogaster.UCSC.dm2_1.4.0
## [23] BSgenome_1.70.1 rtracklayer_1.62.0
## [25] BiocIO_1.12.0 Biostrings_2.70.1
## [27] XVector_0.42.0 rWSBIM1207_0.1.17
## [29] airway_1.22.0 SummarizedExperiment_1.32.0
## [31] Biobase_2.62.0 GenomicRanges_1.54.1
## [33] GenomeInfoDb_1.38.1 IRanges_2.36.0
## [35] S4Vectors_0.40.2 BiocGenerics_0.48.1
## [37] MatrixGenerics_1.14.0 matrixStats_1.1.0
## [39] BiocStyle_2.30.0 lattice_0.22-5
## [41] patchwork_1.1.3 ggbeeswarm_0.7.2
## [43] plotly_4.10.3 Hmisc_5.1-1
## [45] lubridate_1.9.3 forcats_1.0.0
## [47] stringr_1.5.1 dplyr_1.1.4
## [49] purrr_1.0.2 readr_2.1.4
## [51] tidyr_1.3.0 tibble_3.2.1
## [53] ggplot2_3.4.4 tidyverse_2.0.0
## [55] rWSBIM1322_0.3.2
##
## loaded via a namespace (and not attached):
## [1] segmented_1.6-4 bitops_1.0-7 httr_1.4.7
## [4] RColorBrewer_1.1-3 doParallel_1.0.17 tools_4.3.1
## [7] backports_1.4.1 utf8_1.2.4 R6_2.5.1
## [10] lazyeval_0.2.2 mgcv_1.9-0 GetoptLong_1.0.5
## [13] withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3
## [16] preprocessCore_1.64.0 cli_3.6.1 Cairo_1.6-1
## [19] isoband_0.2.7 labeling_0.4.3 sass_0.4.7
## [22] mvtnorm_1.2-3 randomForest_4.7-1.1 proxy_0.4-27
## [25] Rsamtools_2.18.0 foreign_0.8-85 parallelly_1.36.0
## [28] plotrix_3.8-4 limma_3.58.1 rstudioapi_0.15.0
## [31] impute_1.76.0 RSQLite_2.3.3 FNN_1.1.3.2
## [34] shape_1.4.6 generics_0.1.3 vroom_1.6.4
## [37] gtools_3.9.5 car_3.1-2 dendextend_1.17.1
## [40] Matrix_1.6-3 MALDIquant_1.22.1 fansi_1.0.5
## [43] abind_1.4-5 lifecycle_1.0.4 yaml_2.3.7
## [46] carData_3.0-5 recipes_1.0.8 SparseArray_1.2.2
## [49] BiocFileCache_2.11.1 blob_1.2.4 crayon_1.5.2
## [52] KEGGREST_1.42.0 magick_2.8.1 pillar_1.9.0
## [55] knitr_1.45 rjson_0.2.21 lpSolve_5.6.19
## [58] future.apply_1.11.0 codetools_0.2-19 glue_1.6.2
## [61] pcaMethods_1.94.0 data.table_1.14.8 vctrs_0.6.4
## [64] png_0.1-8 gtable_0.3.4 kernlab_0.9-32
## [67] cachem_1.0.8 gower_1.0.1 xfun_0.41
## [70] prodlim_2023.08.28 S4Arrays_1.2.0 coda_0.19-4
## [73] survival_3.5-7 ncdf4_1.21 timeDate_4022.108
## [76] iterators_1.0.14 hardhat_1.3.0 lava_1.7.3
## [79] statmod_1.5.0 ipred_0.9-14 nlme_3.1-163
## [82] bit64_4.0.5 progress_1.2.2 filelock_1.0.2
## [85] LaplacesDemon_16.1.6 bslib_0.6.0 affyio_1.72.0
## [88] vipor_0.4.5 rpart_4.1.21 colorspace_2.1-0
## [91] DBI_1.1.3 nnet_7.3-19 tidyselect_1.2.0
## [94] bit_4.0.5 compiler_4.3.1 curl_5.1.0
## [97] graph_1.80.0 htmlTable_2.4.2 xml2_1.3.5
## [100] DelayedArray_0.28.0
## [ reached getOption("max.print") -- omitted 70 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", "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: 2023-11-27 using R version 4.3.1 Patched (2023-07-10 r84676)