Loading required package: methylKit Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:lubridate': intersect, setdiff, union The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:data.table': first, second The following objects are masked from 'package:lubridate': second, second<- The following objects are masked from 'package:dplyr': first, rename The following object is masked from 'package:tidyr': expand The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:data.table': shift The following object is masked from 'package:lubridate': %within% The following objects are masked from 'package:dplyr': collapse, desc, slice The following object is masked from 'package:purrr': reduce Loading required package: GenomeInfoDb Attaching package: 'methylKit' The following object is masked from 'package:dplyr': select The following object is masked from 'package:tidyr': unite All CpG: 250458 features, 24 oysters All gene: 34052 features, 24 oysters DropGeno4 CpG: 295226 features, 20 oysters DropGeno4 gene: 34678 features, 20 oysters sampleSet features nFeatures genoK test 1 All CpG 250458 1 PERMANOVA (marginal) 2 All CpG 250458 1 PERMANOVA (marginal) 3 All CpG 250458 1 PERMANOVA (marginal) 4 All CpG 250458 1 PERMANOVA (marginal) 5 All CpG 250458 1 PERMANOVA (marginal) 6 All CpG 250458 1 PERMANOVA (marginal) 7 All CpG 250458 1 varpart (adjusted R2) 8 All CpG 250458 1 varpart (adjusted R2) 9 All CpG 250458 1 varpart (adjusted R2) 10 All CpG 250458 1 varpart (adjusted R2) 11 All CpG 250458 3 PERMANOVA (marginal) 12 All CpG 250458 3 PERMANOVA (marginal) 13 All CpG 250458 3 PERMANOVA (marginal) 14 All CpG 250458 3 PERMANOVA (marginal) 15 All CpG 250458 3 PERMANOVA (marginal) 16 All CpG 250458 3 PERMANOVA (marginal) 17 All CpG 250458 3 PERMANOVA (marginal) 18 All CpG 250458 3 PERMANOVA (marginal) 19 All CpG 250458 3 varpart (adjusted R2) 20 All CpG 250458 3 varpart (adjusted R2) 21 All CpG 250458 3 varpart (adjusted R2) 22 All CpG 250458 3 varpart (adjusted R2) 23 All CpG 250458 5 PERMANOVA (marginal) 24 All CpG 250458 5 PERMANOVA (marginal) 25 All CpG 250458 5 PERMANOVA (marginal) 26 All CpG 250458 5 PERMANOVA (marginal) 27 All CpG 250458 5 PERMANOVA (marginal) 28 All CpG 250458 5 PERMANOVA (marginal) 29 All CpG 250458 5 PERMANOVA (marginal) 30 All CpG 250458 5 PERMANOVA (marginal) 31 All CpG 250458 5 PERMANOVA (marginal) 32 All CpG 250458 5 PERMANOVA (marginal) 33 All CpG 250458 5 varpart (adjusted R2) 34 All CpG 250458 5 varpart (adjusted R2) 35 All CpG 250458 5 varpart (adjusted R2) 36 All CpG 250458 5 varpart (adjusted R2) 37 All CpG 250458 NA Mantel 38 All CpG 250458 NA partial Mantel (| treatment) 39 All gene 34052 1 PERMANOVA (marginal) 40 All gene 34052 1 PERMANOVA (marginal) 41 All gene 34052 1 PERMANOVA (marginal) 42 All gene 34052 1 PERMANOVA (marginal) 43 All gene 34052 1 PERMANOVA (marginal) 44 All gene 34052 1 PERMANOVA (marginal) 45 All gene 34052 1 varpart (adjusted R2) 46 All gene 34052 1 varpart (adjusted R2) 47 All gene 34052 1 varpart (adjusted R2) 48 All gene 34052 1 varpart (adjusted R2) 49 All gene 34052 3 PERMANOVA (marginal) 50 All gene 34052 3 PERMANOVA (marginal) 51 All gene 34052 3 PERMANOVA (marginal) 52 All gene 34052 3 PERMANOVA (marginal) 53 All gene 34052 3 PERMANOVA (marginal) 54 All gene 34052 3 PERMANOVA (marginal) 55 All gene 34052 3 PERMANOVA (marginal) 56 All gene 34052 3 PERMANOVA (marginal) 57 All gene 34052 3 varpart (adjusted R2) 58 All gene 34052 3 varpart (adjusted R2) 59 All gene 34052 3 varpart (adjusted R2) 60 All gene 34052 3 varpart (adjusted R2) 61 All gene 34052 5 PERMANOVA (marginal) 62 All gene 34052 5 PERMANOVA (marginal) 63 All gene 34052 5 PERMANOVA (marginal) 64 All gene 34052 5 PERMANOVA (marginal) 65 All gene 34052 5 PERMANOVA (marginal) 66 All gene 34052 5 PERMANOVA (marginal) 67 All gene 34052 5 PERMANOVA (marginal) 68 All gene 34052 5 PERMANOVA (marginal) 69 All gene 34052 5 PERMANOVA (marginal) 70 All gene 34052 5 PERMANOVA (marginal) 71 All gene 34052 5 varpart (adjusted R2) 72 All gene 34052 5 varpart (adjusted R2) 73 All gene 34052 5 varpart (adjusted R2) 74 All gene 34052 5 varpart (adjusted R2) 75 All gene 34052 NA Mantel 76 All gene 34052 NA partial Mantel (| treatment) 77 DropGeno4 CpG 295226 1 PERMANOVA (marginal) 78 DropGeno4 CpG 295226 1 PERMANOVA (marginal) 79 DropGeno4 CpG 295226 1 PERMANOVA (marginal) 80 DropGeno4 CpG 295226 1 PERMANOVA (marginal) 81 DropGeno4 CpG 295226 1 PERMANOVA (marginal) 82 DropGeno4 CpG 295226 1 PERMANOVA (marginal) 83 DropGeno4 CpG 295226 1 varpart (adjusted R2) 84 DropGeno4 CpG 295226 1 varpart (adjusted R2) 85 DropGeno4 CpG 295226 1 varpart (adjusted R2) 86 DropGeno4 CpG 295226 1 varpart (adjusted R2) 87 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 88 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 89 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 90 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 91 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 92 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 93 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 94 DropGeno4 CpG 295226 3 PERMANOVA (marginal) 95 DropGeno4 CpG 295226 3 varpart (adjusted R2) 96 DropGeno4 CpG 295226 3 varpart (adjusted R2) 97 DropGeno4 CpG 295226 3 varpart (adjusted R2) 98 DropGeno4 CpG 295226 3 varpart (adjusted R2) 99 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 100 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 101 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 102 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 103 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 104 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 105 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 106 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 107 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 108 DropGeno4 CpG 295226 5 PERMANOVA (marginal) 109 DropGeno4 CpG 295226 5 varpart (adjusted R2) 110 DropGeno4 CpG 295226 5 varpart (adjusted R2) 111 DropGeno4 CpG 295226 5 varpart (adjusted R2) 112 DropGeno4 CpG 295226 5 varpart (adjusted R2) 113 DropGeno4 CpG 295226 NA Mantel 114 DropGeno4 CpG 295226 NA partial Mantel (| treatment) 115 DropGeno4 gene 34678 1 PERMANOVA (marginal) 116 DropGeno4 gene 34678 1 PERMANOVA (marginal) 117 DropGeno4 gene 34678 1 PERMANOVA (marginal) 118 DropGeno4 gene 34678 1 PERMANOVA (marginal) 119 DropGeno4 gene 34678 1 PERMANOVA (marginal) 120 DropGeno4 gene 34678 1 PERMANOVA (marginal) 121 DropGeno4 gene 34678 1 varpart (adjusted R2) 122 DropGeno4 gene 34678 1 varpart (adjusted R2) 123 DropGeno4 gene 34678 1 varpart (adjusted R2) 124 DropGeno4 gene 34678 1 varpart (adjusted R2) 125 DropGeno4 gene 34678 3 PERMANOVA (marginal) 126 DropGeno4 gene 34678 3 PERMANOVA (marginal) 127 DropGeno4 gene 34678 3 PERMANOVA (marginal) 128 DropGeno4 gene 34678 3 PERMANOVA (marginal) 129 DropGeno4 gene 34678 3 PERMANOVA (marginal) 130 DropGeno4 gene 34678 3 PERMANOVA (marginal) 131 DropGeno4 gene 34678 3 PERMANOVA (marginal) 132 DropGeno4 gene 34678 3 PERMANOVA (marginal) 133 DropGeno4 gene 34678 3 varpart (adjusted R2) 134 DropGeno4 gene 34678 3 varpart (adjusted R2) 135 DropGeno4 gene 34678 3 varpart (adjusted R2) 136 DropGeno4 gene 34678 3 varpart (adjusted R2) 137 DropGeno4 gene 34678 5 PERMANOVA (marginal) 138 DropGeno4 gene 34678 5 PERMANOVA (marginal) 139 DropGeno4 gene 34678 5 PERMANOVA (marginal) 140 DropGeno4 gene 34678 5 PERMANOVA (marginal) 141 DropGeno4 gene 34678 5 PERMANOVA (marginal) 142 DropGeno4 gene 34678 5 PERMANOVA (marginal) 143 DropGeno4 gene 34678 5 PERMANOVA (marginal) 144 DropGeno4 gene 34678 5 PERMANOVA (marginal) 145 DropGeno4 gene 34678 5 PERMANOVA (marginal) 146 DropGeno4 gene 34678 5 PERMANOVA (marginal) 147 DropGeno4 gene 34678 5 varpart (adjusted R2) 148 DropGeno4 gene 34678 5 varpart (adjusted R2) 149 DropGeno4 gene 34678 5 varpart (adjusted R2) 150 DropGeno4 gene 34678 5 varpart (adjusted R2) 151 DropGeno4 gene 34678 NA Mantel 152 DropGeno4 gene 34678 NA partial Mantel (| treatment) term R2 F p 1 ploidy 0.0450047367 1.0830293 0.1553 2 pH 0.0366785090 0.8826604 0.9456 3 ploidyXpH 0.0489412839 1.1777614 0.0095 4 PC1 0.0704767831 1.6960085 0.0030 5 Residual 0.7895354566 NA NA 6 Total 1.0000000000 NA NA 7 genotype only [a] 0.0332606282 NA NA 8 shared [b] 0.0064929140 NA NA 9 treatment only [c] 0.0044930103 NA NA 10 residual [d] 0.9557534475 NA NA 11 ploidy 0.0463610539 1.1709812 0.0217 12 pH 0.0351763425 0.8884792 0.9271 13 ploidyXpH 0.0450776816 1.1385659 0.0583 14 PC1 0.0705133910 1.7810176 0.0004 15 PC2 0.0657783781 1.6614213 0.0032 16 PC3 0.0505756498 1.2774328 0.0363 17 Residual 0.6730577270 NA NA 18 Total 1.0000000000 NA NA 19 genotype only [a] 0.0784065627 NA NA 20 shared [b] 0.0095464162 NA NA 21 treatment only [c] 0.0014395081 NA NA 22 residual [d] 0.9106075130 NA NA 23 ploidy 0.0482236951 1.2463186 0.0087 24 pH 0.0350944358 0.9069991 0.8346 25 ploidyXpH 0.0475499125 1.2289050 0.0474 26 PC1 0.0695449469 1.7973563 0.0002 27 PC2 0.0656032128 1.6954841 0.0018 28 PC3 0.0498200298 1.2875751 0.0296 29 PC4 0.0462847497 1.1962075 0.0661 30 PC5 0.0468379153 1.2105038 0.0707 31 Residual 0.5803936580 NA NA 32 Total 1.0000000000 NA NA 33 genotype only [a] 0.0990771334 NA NA 34 shared [b] 0.0149967906 NA NA 35 treatment only [c] -0.0040108662 NA NA 36 residual [d] 0.8899369423 NA NA 37 genotype distance vs methylation distance 0.7308303249 NA 0.0001 38 genotype distance vs methylation distance 0.7314343059 NA 0.0001 39 ploidy 0.0448167701 1.1049817 0.1820 40 pH 0.0319963619 0.7888876 0.9825 41 ploidyXpH 0.0526433280 1.2979498 0.0068 42 PC1 0.0853276264 2.1037988 0.0009 43 Residual 0.7706178379 NA NA 44 Total 1.0000000000 NA NA 45 genotype only [a] 0.0514841117 NA NA 46 shared [b] 0.0085285863 NA NA 47 treatment only [c] 0.0071341297 NA NA 48 residual [d] 0.9328531722 NA NA 49 ploidy 0.0457202215 1.2118548 0.0487 50 pH 0.0302763979 0.8025026 0.9674 51 ploidyXpH 0.0461878588 1.2242499 0.0470 52 PC1 0.0857429514 2.2726925 0.0002 53 PC2 0.0761960085 2.0196424 0.0011 54 PC3 0.0529462901 1.4033881 0.0352 55 Residual 0.6413670884 NA NA 56 Total 1.0000000000 NA NA 57 genotype only [a] 0.1166053408 NA NA 58 shared [b] 0.0112316395 NA NA 59 treatment only [c] 0.0044310766 NA NA 60 residual [d] 0.8677319432 NA NA 61 ploidy 0.0471170263 1.2941598 0.0265 62 pH 0.0299126955 0.8216097 0.9194 63 ploidyXpH 0.0478647336 1.3146970 0.0525 64 PC1 0.0843901022 2.3179365 0.0001 65 PC2 0.0759366092 2.0857450 0.0007 66 PC3 0.0517179597 1.4205332 0.0266 67 PC4 0.0511086868 1.4037984 0.0277 68 PC5 0.0442319734 1.2149162 0.1256 69 Residual 0.5461113960 NA NA 70 Total 1.0000000000 NA NA 71 genotype only [a] 0.1469664767 NA NA 72 shared [b] 0.0153781277 NA NA 73 treatment only [c] 0.0002845884 NA NA 74 residual [d] 0.8373708072 NA NA 75 genotype distance vs methylation distance 0.7679171245 NA 0.0001 76 genotype distance vs methylation distance 0.7681686711 NA 0.0001 77 ploidy 0.0544775491 1.0572895 0.1499 78 pH 0.0491107039 0.9531309 0.8039 79 ploidyXpH 0.0532092607 1.0326748 0.2567 80 PC1 0.0679809908 1.3193617 0.0001 81 Residual 0.7728850164 NA NA 82 Total 1.0000000000 NA NA 83 genotype only [a] 0.0195406961 NA NA 84 shared [b] 0.0019108153 NA NA 85 treatment only [c] -0.0004391988 NA NA 86 residual [d] 0.9789876874 NA NA 87 ploidy 0.0541503996 1.0801437 0.0845 88 pH 0.0485595179 0.9686218 0.7026 89 ploidyXpH 0.0521596512 1.0404341 0.2233 90 PC1 0.0678914725 1.3542384 0.0001 91 PC2 0.0624413332 1.2455239 0.0002 92 PC3 0.0586214609 1.1693285 0.0100 93 Residual 0.6517236297 NA NA 94 Total 1.0000000000 NA NA 95 genotype only [a] 0.0460092325 NA NA 96 shared [b] 0.0053140712 NA NA 97 treatment only [c] -0.0038424547 NA NA 98 residual [d] 0.9525191511 NA NA 99 ploidy 0.0489933123 0.9992020 0.4932 100 pH 0.0492045504 1.0035101 0.4508 101 ploidyXpH 0.0510834233 1.0418291 0.2337 102 PC1 0.0665271250 1.3567982 0.0001 103 PC2 0.0622792753 1.2701647 0.0001 104 PC3 0.0586866572 1.1968945 0.0043 105 PC4 0.0581585973 1.1861249 0.0040 106 PC5 0.0538347595 1.0979417 0.0534 107 Residual 0.5393568478 NA NA 108 Total 1.0000000000 NA NA 109 genotype only [a] 0.0669120101 NA NA 110 shared [b] 0.0030606365 NA NA 111 treatment only [c] -0.0015890200 NA NA 112 residual [d] 0.9316163734 NA NA 113 genotype distance vs methylation distance 0.2772752125 NA 0.0006 114 genotype distance vs methylation distance 0.2796534689 NA 0.0007 115 ploidy 0.0545817990 1.0725549 0.2234 116 pH 0.0451758978 0.8877250 0.8895 117 ploidyXpH 0.0531247489 1.0439232 0.3008 118 PC1 0.0783232253 1.5390837 0.0001 119 Residual 0.7633427641 NA NA 120 Total 1.0000000000 NA NA 121 genotype only [a] 0.0325775279 NA NA 122 shared [b] 0.0001705562 NA NA 123 treatment only [c] 0.0003510814 NA NA 124 residual [d] 0.9669008345 NA NA 125 ploidy 0.0530628529 1.1048829 0.1459 126 pH 0.0440192661 0.9165759 0.8009 127 ploidyXpH 0.0508764889 1.0593581 0.2555 128 PC1 0.0779041148 1.6221314 0.0001 129 PC2 0.0755194095 1.5724767 0.0001 130 PC3 0.0633667536 1.3194323 0.0073 131 Residual 0.6243350396 NA NA 132 Total 1.0000000000 NA NA 133 genotype only [a] 0.0869886891 NA NA 134 shared [b] 0.0054703088 NA NA 135 treatment only [c] -0.0049486711 NA NA 136 residual [d] 0.9124896733 NA NA 137 ploidy 0.0478933674 1.0278410 0.3715 138 pH 0.0452497666 0.9711066 0.5935 139 ploidyXpH 0.0480543878 1.0312966 0.3580 140 PC1 0.0756877648 1.6243374 0.0001 141 PC2 0.0754077021 1.6183269 0.0001 142 PC3 0.0634615740 1.3619507 0.0032 143 PC4 0.0589769524 1.2657061 0.0143 144 PC5 0.0531612219 1.1408946 0.0910 145 Residual 0.5125569584 NA NA 146 Total 1.0000000000 NA NA 147 genotype only [a] 0.1141527070 NA NA 148 shared [b] 0.0021363540 NA NA 149 treatment only [c] -0.0016147164 NA NA 150 residual [d] 0.8853256554 NA NA 151 genotype distance vs methylation distance 0.4113696108 NA 0.0001 152 genotype distance vs methylation distance 0.4116623430 NA 0.0001 sampleSet genoK features median_R2treatment median_R2genotype 1 All 3 CpG 0.1200629 0.1569825 2 All 3 gene 0.1215878 0.1542448 3 DropGeno4 3 CpG 0.1364849 0.1535501 4 DropGeno4 3 gene 0.1391935 0.1576992 median_uniqueTreatment median_uniqueGenotype median_shared fracGenotypeP0.01 1 0.1093560 0.1482245 0.007417103 0.05048351 2 0.1086760 0.1455047 0.009747641 0.06443087 3 0.1336689 0.1512573 0.001876878 0.02178331 4 0.1341266 0.1543670 0.003071338 0.02292520 fracTreatmentP0.01 1 0.01198604 2 0.01060143 3 0.01123207 4 0.01075610 sampleSet features null median_uniqueTreatment 1 All CpG genotype shuffled 0.1190101 2 All CpG treatment labels shuffled 0.1010665 3 All gene genotype shuffled 0.1199415 4 All gene treatment labels shuffled 0.1018812 5 DropGeno4 CpG genotype shuffled 0.1356276 6 DropGeno4 CpG treatment labels shuffled 0.1291804 7 DropGeno4 gene genotype shuffled 0.1379073 8 DropGeno4 gene treatment labels shuffled 0.1291598 median_uniqueGenotype fracGenotypeP0.01 fracTreatmentP0.01 1 0.1066895 0.011121625 0.011584777 2 0.1506610 0.050385693 0.009382811 3 0.1030223 0.013523435 0.010674850 4 0.1491118 0.064959474 0.008398919 5 0.1329807 0.009741689 0.010659630 6 0.1503136 0.020699396 0.009904277 7 0.1325883 0.009631467 0.009804487 8 0.1541230 0.022391718 0.009544956 R version 4.4.3 (2025-02-28) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 24.04.4 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0 locale: [1] C time zone: Etc/UTC tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] methylKit_1.32.1 GenomicRanges_1.58.0 GenomeInfoDb_1.42.3 [4] IRanges_2.40.1 S4Vectors_0.44.0 BiocGenerics_0.52.0 [7] vegan_2.7-5 permute_0.9-10 data.table_1.17.0 [10] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 [13] dplyr_1.1.4 purrr_1.0.4 readr_2.1.5 [16] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.2 [19] tidyverse_2.0.0 loaded via a namespace (and not attached): [1] tidyselect_1.2.1 farver_2.1.2 [3] R.utils_2.13.0 Biostrings_2.74.1 [5] bitops_1.0-9 RCurl_1.98-1.19 [7] GenomicAlignments_1.42.0 XML_3.99-0.18 [9] timechange_0.3.0 lifecycle_1.0.4 [11] cluster_2.1.8.1 statmod_1.5.2 [13] magrittr_2.0.3 compiler_4.4.3 [15] rlang_1.1.5 tools_4.4.3 [17] yaml_2.3.10 rtracklayer_1.66.0 [19] labeling_0.4.3 S4Arrays_1.6.0 [21] bit_4.6.0 mclust_6.1.3 [23] curl_6.2.2 DelayedArray_0.32.0 [25] plyr_1.8.9 abind_1.4-8 [27] BiocParallel_1.40.2 withr_3.0.2 [29] numDeriv_2016.8-1.1 R.oo_1.27.1 [31] grid_4.4.3 colorspace_2.1-1 [33] scales_1.3.0 gtools_3.9.5 [35] MASS_7.3-65 SummarizedExperiment_1.36.0 [37] bbmle_1.0.25.1 cli_3.6.4 [39] mvtnorm_1.4-1 crayon_1.5.3 [41] ragg_1.3.3 generics_0.1.3 [43] rjson_0.2.23 httr_1.4.7 [45] reshape2_1.4.4 tzdb_0.5.0 [47] bdsmatrix_1.3-7 qvalue_2.38.0 [49] zlibbioc_1.52.0 splines_4.4.3 [51] parallel_4.4.3 XVector_0.46.0 [53] restfulr_0.0.17 matrixStats_1.5.0 [55] vctrs_0.6.5 Matrix_1.7-3 [57] jsonlite_2.0.0 hms_1.1.3 [59] bit64_4.6.0-1 systemfonts_1.2.2 [61] fastseg_1.52.0 limma_3.62.2 [63] glue_1.8.0 emdbook_1.3.14 [65] codetools_0.2-20 stringi_1.8.7 [67] gtable_0.3.6 BiocIO_1.16.0 [69] UCSC.utils_1.2.0 munsell_0.5.1 [71] pillar_1.10.2 GenomeInfoDbData_1.2.13 [73] R6_2.6.1 textshaping_1.0.0 [75] vroom_1.6.5 lattice_0.22-7 [77] Biobase_2.66.0 R.methodsS3_1.8.2 [79] Rsamtools_2.22.0 Rcpp_1.0.14 [81] SparseArray_1.6.2 coda_0.19-4.1 [83] nlme_3.1-168 mgcv_1.9-3 [85] MatrixGenerics_1.18.1 pkgconfig_2.0.3