The following packages have been used to generate this document.
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/lgatto/bin/Rpatched/lib/R/lib/libRblas.so
## LAPACK: /home/lgatto/bin/Rpatched/lib/R/lib/libRlapack.so; LAPACK version 3.12.0
##
## 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_2.20.0 class_7.3-22
## [5] pRoloc_1.45.2 BiocParallel_1.38.0
## [7] MLInterfaces_1.84.0 cluster_2.1.6
## [9] annotate_1.82.0 XML_3.99-0.17
## [11] AnnotationDbi_1.66.0 bioDist_1.76.0
## [13] KernSmooth_2.23-24 factoextra_1.0.7
## [15] pRolocdata_1.43.3 MSnbase_2.30.1
## [17] ProtGenerics_1.36.0 mzR_2.38.0
## [19] Rcpp_1.0.13 QFeatures_1.14.2
## [21] MultiAssayExperiment_1.30.3 BSgenome.Dmelanogaster.UCSC.dm2_1.4.0
## [23] BSgenome_1.72.0 rtracklayer_1.64.0
## [25] BiocIO_1.14.0 Biostrings_2.72.1
## [27] XVector_0.44.0 rWSBIM1207_0.1.19
## [29] airway_1.24.0 SummarizedExperiment_1.34.0
## [31] Biobase_2.64.0 GenomicRanges_1.56.2
## [33] GenomeInfoDb_1.40.1 IRanges_2.38.1
## [35] S4Vectors_0.42.1 BiocGenerics_0.50.0
## [37] MatrixGenerics_1.16.0 matrixStats_1.4.1
## [39] BiocStyle_2.32.1 lattice_0.22-6
## [41] patchwork_1.3.0 ggbeeswarm_0.7.2
## [43] plotly_4.10.4 Hmisc_5.1-3
## [45] lubridate_1.9.3 forcats_1.0.0
## [47] stringr_1.5.1 dplyr_1.1.4
## [49] purrr_1.0.2 readr_2.1.5
## [51] tidyr_1.3.1 tibble_3.2.1
## [53] ggplot2_3.5.1 tidyverse_2.0.0
## [55] rWSBIM1322_0.3.2
##
## loaded via a namespace (and not attached):
## [1] segmented_2.1-2 bitops_1.0-9 httr_1.4.7
## [4] RColorBrewer_1.1-3 doParallel_1.0.17 tools_4.4.1
## [7] backports_1.5.0 utf8_1.2.4 R6_2.5.1
## [10] lazyeval_0.2.2 mgcv_1.9-1 GetoptLong_1.0.5
## [13] withr_3.0.1 prettyunits_1.2.0 gridExtra_2.3
## [16] preprocessCore_1.66.0 cli_3.6.3 Cairo_1.6-2
## [19] isoband_0.2.7 labeling_0.4.3 sass_0.4.9
## [22] mvtnorm_1.3-1 randomForest_4.7-1.2 proxy_0.4-27
## [25] Rsamtools_2.20.0 foreign_0.8-87 parallelly_1.38.0
## [28] plotrix_3.8-4 limma_3.60.6 rstudioapi_0.17.0
## [31] impute_1.78.0 RSQLite_2.3.7 FNN_1.1.4.1
## [34] shape_1.4.6.1 generics_0.1.3 vroom_1.6.5
## [37] gtools_3.9.5 car_3.1-3 dendextend_1.18.1
## [40] Matrix_1.7-1 MALDIquant_1.22.3 fansi_1.0.6
## [43] abind_1.4-8 lifecycle_1.0.4 yaml_2.3.10
## [46] carData_3.0-5 recipes_1.1.0 SparseArray_1.4.8
## [49] BiocFileCache_2.12.0 blob_1.2.4 crayon_1.5.3
## [52] PSMatch_1.8.0 KEGGREST_1.44.1 magick_2.8.5
## [55] pillar_1.9.0 knitr_1.48 rjson_0.2.23
## [58] lpSolve_5.6.21 future.apply_1.11.2 codetools_0.2-20
## [61] glue_1.8.0 pcaMethods_1.96.0 data.table_1.16.2
## [64] vctrs_0.6.5 png_0.1-8 gtable_0.3.5
## [67] kernlab_0.9-33 cachem_1.1.0 gower_1.0.1
## [70] xfun_0.48 prodlim_2024.06.25 S4Arrays_1.4.1
## [73] coda_0.19-4.1 survival_3.7-0 ncdf4_1.23
## [76] timeDate_4041.110 iterators_1.0.14 hardhat_1.4.0
## [79] lava_1.8.0 statmod_1.5.0 ipred_0.9-15
## [82] nlme_3.1-166 bit64_4.5.2 progress_1.2.3
## [85] filelock_1.0.3 LaplacesDemon_16.1.6 bslib_0.8.0
## [88] affyio_1.74.0 vipor_0.4.7 rpart_4.1.23
## [91] colorspace_2.1-1 DBI_1.2.3 nnet_7.3-19
## [94] tidyselect_1.2.1 bit_4.5.0 compiler_4.4.1
## [97] curl_5.2.3 graph_1.82.0 httr2_1.0.5
## [100] htmlTable_2.4.3
## [ reached getOption("max.print") -- omitted 73 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: 2024-10-28 using R version 4.4.1 (2024-06-14)