- Data summary
- Number of hits from each method
- Volcano plot
- Histogram of p-value/BH
- Boxplot of log2mean of hits
- Boxplot of gene expression frequency of hits
- Heatmap of top hits
- FC, Mean, Mean difference plot
- Enrichment analysis
- GO object
- enrichKEGG object
group2_19
Chih-Hsuan Wu
Last updated: 2023-05-18
Checks: 5 2
Knit directory: DEanalysis/
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Data summary
Number of hits from each method
Volcano plot
Histogram of p-value/BH
Boxplot of log2mean of hits
Boxplot of gene expression frequency of hits
Heatmap of top hits
FC, Mean, Mean difference plot
Enrichment analysis
GO object
enrichKEGG object
sessionInfo()R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] DESeq2_1.38.3 pathview_1.38.0
[3] org.Hs.eg.db_3.16.0 AnnotationDbi_1.60.2
[5] enrichplot_1.18.4 clusterProfiler_4.6.2
[7] reshape_0.8.9 gridExtra_2.3
[9] pheatmap_1.0.12 SingleCellExperiment_1.20.1
[11] SummarizedExperiment_1.28.0 Biobase_2.58.0
[13] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[15] IRanges_2.32.0 S4Vectors_0.36.2
[17] BiocGenerics_0.44.0 MatrixGenerics_1.10.0
[19] matrixStats_0.63.0 ggpubr_0.6.0
[21] dplyr_1.1.2 ggplot2_3.4.2
loaded via a namespace (and not attached):
[1] shadowtext_0.1.2 backports_1.4.1 fastmatch_1.1-3
[4] workflowr_1.7.0 plyr_1.8.8 igraph_1.4.2
[7] lazyeval_0.2.2 splines_4.2.2 BiocParallel_1.32.6
[10] digest_0.6.31 yulab.utils_0.0.6 htmltools_0.5.5
[13] GOSemSim_2.24.0 viridis_0.6.3 GO.db_3.16.0
[16] fansi_1.0.4 magrittr_2.0.3 memoise_2.0.1
[19] annotate_1.76.0 Biostrings_2.66.0 graphlayouts_1.0.0
[22] colorspace_2.1-0 blob_1.2.4 ggrepel_0.9.3
[25] xfun_0.39 crayon_1.5.2 RCurl_1.98-1.12
[28] jsonlite_1.8.4 graph_1.76.0 scatterpie_0.1.9
[31] ape_5.7-1 glue_1.6.2 polyclip_1.10-4
[34] gtable_0.3.3 zlibbioc_1.44.0 XVector_0.38.0
[37] DelayedArray_0.24.0 car_3.1-2 Rgraphviz_2.42.0
[40] abind_1.4-5 scales_1.2.1 DOSE_3.24.2
[43] DBI_1.1.3 rstatix_0.7.2 Rcpp_1.0.10
[46] xtable_1.8-4 viridisLite_0.4.2 gridGraphics_0.5-1
[49] tidytree_0.4.2 bit_4.0.5 httr_1.4.5
[52] fgsea_1.24.0 RColorBrewer_1.1-3 XML_3.99-0.14
[55] pkgconfig_2.0.3 farver_2.1.1 sass_0.4.5
[58] locfit_1.5-9.7 utf8_1.2.3 labeling_0.4.2
[61] ggplotify_0.1.0 tidyselect_1.2.0 rlang_1.1.1
[64] reshape2_1.4.4 later_1.3.0 munsell_0.5.0
[67] tools_4.2.2 cachem_1.0.8 downloader_0.4
[70] cli_3.6.1 generics_0.1.3 RSQLite_2.3.1
[73] gson_0.1.0 broom_1.0.4 evaluate_0.20
[76] stringr_1.5.0 fastmap_1.1.1 yaml_2.3.7
[79] ggtree_3.6.2 knitr_1.42 bit64_4.0.5
[82] fs_1.6.2 tidygraph_1.2.3 purrr_1.0.1
[85] KEGGREST_1.38.0 ggraph_2.1.0 nlme_3.1-162
[88] KEGGgraph_1.58.3 aplot_0.1.10 compiler_4.2.2
[91] rstudioapi_0.14 png_0.1-8 ggsignif_0.6.4
[94] treeio_1.22.0 geneplotter_1.76.0 tibble_3.2.1
[97] tweenr_2.0.2 bslib_0.4.2 stringi_1.7.12
[100] highr_0.10 lattice_0.21-8 Matrix_1.5-4
[103] vctrs_0.6.2 pillar_1.9.0 lifecycle_1.0.3
[106] jquerylib_0.1.4 data.table_1.14.8 cowplot_1.1.1
[109] bitops_1.0-7 httpuv_1.6.9 patchwork_1.1.2
[112] qvalue_2.30.0 R6_2.5.1 promises_1.2.0.1
[115] codetools_0.2-19 MASS_7.3-59 rprojroot_2.0.3
[118] withr_2.5.0 GenomeInfoDbData_1.2.9 parallel_4.2.2
[121] grid_4.2.2 ggfun_0.0.9 tidyr_1.3.0
[124] HDO.db_0.99.1 rmarkdown_2.21 carData_3.0-5
[127] ggnewscale_0.4.8 git2r_0.32.0 ggforce_0.4.1