This task prepares the R environment by loading all required libraries for RNA-seq processing, methylation analysis, statistical modeling, pathway enrichment, and network inference.
# RNA-seq analysis
library(DESeq2)
library(edgeR)
library(vsn)
# General data wrangling
library(tidyverse)
library(dplyr)
library(genefilter)
# Statistical testing
library(multtest)
library(DescTools)
# Visualization and PCA
library(ggfortify)
library(factoextra)
# Methylation analysis
library(minfi)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
# Pathway and enrichment
library(clusterProfiler)
library(org.Hs.eg.db)
library(AnnotationDbi)
# Network inference
library(GeneNet)
# Optional: Check session info to confirm everything loaded
sessionInfo()## R version 4.4.1 (2024-06-14 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows 11 x64 (build 26100)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=Arabic_Egypt.utf8 LC_CTYPE=Arabic_Egypt.utf8
## [3] LC_MONETARY=Arabic_Egypt.utf8 LC_NUMERIC=C
## [5] LC_TIME=Arabic_Egypt.utf8
##
## time zone: Africa/Cairo
## tzcode source: internal
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] GeneNet_1.2.17
## [2] fdrtool_1.2.18
## [3] longitudinal_1.1.13
## [4] corpcor_1.6.10
## [5] org.Hs.eg.db_3.19.1
## [6] AnnotationDbi_1.66.0
## [7] clusterProfiler_4.12.6
## [8] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
## [9] minfi_1.50.0
## [10] bumphunter_1.46.0
## [11] locfit_1.5-9.9
## [12] iterators_1.0.14
## [13] foreach_1.5.2
## [14] Biostrings_2.72.1
## [15] XVector_0.44.0
## [16] factoextra_1.0.7
## [17] ggfortify_0.4.18
## [18] DescTools_0.99.60
## [19] multtest_2.60.0
## [20] genefilter_1.86.0
## [21] lubridate_1.9.4
## [22] forcats_1.0.0
## [23] stringr_1.5.1
## [24] dplyr_1.1.4
## [25] purrr_1.0.2
## [26] readr_2.1.5
## [27] tidyr_1.3.1
## [28] tibble_3.2.1
## [29] ggplot2_3.5.2
## [30] tidyverse_2.0.0
## [31] vsn_3.72.0
## [32] edgeR_4.2.2
## [33] limma_3.60.6
## [34] DESeq2_1.44.0
## [35] SummarizedExperiment_1.34.0
## [36] Biobase_2.64.0
## [37] MatrixGenerics_1.16.0
## [38] matrixStats_1.3.0
## [39] GenomicRanges_1.56.1
## [40] GenomeInfoDb_1.40.1
## [41] IRanges_2.38.0
## [42] S4Vectors_0.42.0
## [43] BiocGenerics_0.50.0
##
## loaded via a namespace (and not attached):
## [1] fs_1.6.4 bitops_1.0-7
## [3] enrichplot_1.24.0 HDO.db_0.99.1
## [5] httr_1.4.7 RColorBrewer_1.1-3
## [7] tools_4.4.1 doRNG_1.8.6.2
## [9] R6_2.5.1 HDF5Array_1.32.1
## [11] lazyeval_0.2.2 rhdf5filters_1.16.0
## [13] withr_3.0.0 gridExtra_2.3
## [15] base64_2.0.2 preprocessCore_1.66.0
## [17] cli_3.6.3 scatterpie_0.2.3
## [19] sass_0.4.10 mvtnorm_1.3-3
## [21] proxy_0.4-27 askpass_1.2.0
## [23] Rsamtools_2.20.0 yulab.utils_0.2.0
## [25] gson_0.1.0 siggenes_1.78.0
## [27] illuminaio_0.46.0 DOSE_3.30.1
## [29] scrime_1.3.5 readxl_1.4.5
## [31] rstudioapi_0.17.1 RSQLite_2.3.7
## [33] generics_0.1.3 gridGraphics_0.5-1
## [35] BiocIO_1.14.0 GO.db_3.19.1
## [37] Matrix_1.7-0 abind_1.4-5
## [39] lifecycle_1.0.4 yaml_2.3.8
## [41] rhdf5_2.48.0 qvalue_2.36.0
## [43] SparseArray_1.4.8 grid_4.4.1
## [45] blob_1.2.4 crayon_1.5.3
## [47] lattice_0.22-6 haven_2.5.5
## [49] cowplot_1.1.3 GenomicFeatures_1.56.0
## [51] annotate_1.82.0 KEGGREST_1.44.1
## [53] pillar_1.10.1 knitr_1.50
## [55] beanplot_1.3.1 fgsea_1.30.0
## [57] rjson_0.2.21 boot_1.3-30
## [59] gld_2.6.7 codetools_0.2-20
## [61] fastmatch_1.1-4 glue_1.7.0
## [63] ggfun_0.1.5 data.table_1.15.4
## [65] vctrs_0.6.5 png_0.1-8
## [67] treeio_1.28.0 cellranger_1.1.0
## [69] gtable_0.3.5 cachem_1.1.0
## [71] xfun_0.52 S4Arrays_1.4.1
## [73] tidygraph_1.3.1 survival_3.6-4
## [75] statmod_1.5.0 nlme_3.1-164
## [77] ggtree_3.12.0 bit64_4.0.5
## [79] bslib_0.9.0 nor1mix_1.3-3
## [81] affyio_1.74.0 colorspace_2.1-0
## [83] DBI_1.2.3 Exact_3.3
## [85] tidyselect_1.2.1 bit_4.0.5
## [87] compiler_4.4.1 curl_6.4.0
## [89] expm_1.0-0 xml2_1.3.8
## [91] DelayedArray_0.30.1 shadowtext_0.1.3
## [93] rtracklayer_1.64.0 scales_1.3.0
## [95] affy_1.82.0 quadprog_1.5-8
## [97] digest_0.6.35 rmarkdown_2.29
## [99] GEOquery_2.72.0 htmltools_0.5.8.1
## [101] pkgconfig_2.0.3 sparseMatrixStats_1.16.0
## [103] fastmap_1.2.0 rlang_1.1.4
## [105] UCSC.utils_1.0.0 DelayedMatrixStats_1.26.0
## [107] farver_2.1.2 jquerylib_0.1.4
## [109] jsonlite_1.8.8 BiocParallel_1.38.0
## [111] mclust_6.1.1 GOSemSim_2.30.0
## [113] RCurl_1.98-1.14 magrittr_2.0.3
## [115] GenomeInfoDbData_1.2.12 ggplotify_0.1.2
## [117] patchwork_1.2.0 Rhdf5lib_1.26.0
## [119] munsell_0.5.1 Rcpp_1.0.12
## [121] ape_5.8 viridis_0.6.5
## [123] stringi_1.8.4 ggraph_2.2.1
## [125] rootSolve_1.8.2.4 zlibbioc_1.50.0
## [127] MASS_7.3-60.2 plyr_1.8.9
## [129] ggrepel_0.9.5 lmom_3.2
## [131] graphlayouts_1.1.1 splines_4.4.1
## [133] hms_1.1.3 igraph_2.0.3
## [135] rngtools_1.5.2 reshape2_1.4.4
## [137] XML_3.99-0.16.1 evaluate_1.0.4
## [139] BiocManager_1.30.26 tzdb_0.5.0
## [141] tweenr_2.0.3 openssl_2.2.0
## [143] polyclip_1.10-6 reshape_0.8.10
## [145] ggforce_0.4.2 xtable_1.8-4
## [147] restfulr_0.0.15 e1071_1.7-16
## [149] tidytree_0.4.6 viridisLite_0.4.2
## [151] class_7.3-22 aplot_0.2.3
## [153] memoise_2.0.1 GenomicAlignments_1.40.0
## [155] timechange_0.3.0