group8_17
Chih-Hsuan Wu
Last updated: 2023-08-03
Checks: 5 2
Knit directory: DEanalysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 0e93efd | C-HW | 2023-07-25 | upload again |
| html | f314434 | C-HW | 2023-07-25 | add muscat methods |
| html | 7ee9782 | C-HW | 2023-07-13 | add 8_17 |
Histogram of p-value/adj.p-value
Violin plot of gene expression frequency of hits
Heatmap of top hits
Hits in all datasets
| Version | Author | Date |
|---|---|---|
| 7ee9782 | C-HW | 2023-07-13 |
| Version | Author | Date |
|---|---|---|
| 7ee9782 | C-HW | 2023-07-13 |
| Version | Author | Date |
|---|---|---|
| 7ee9782 | C-HW | 2023-07-13 |
Hits in pois_glmm not in MMpoisson
In the MMpoisson model, cell type is considered as a random effect. This approach treats certain aspects of cell type variations as random factors. Consequently, it may obscure the true variation in cell types, limiting its ability to accurately reveal the specific differences between different cell types.
Additionally, the library size is employed as an offset to normalize the counts. That is, the model is considering rate instead of counts. Suppose some genes are highly expressed in one cell type than the other, the absolute difference could be eliminate after accounting for library size. This normalization approach may inadvertently mask certain gene expression differences between cell types.
| Version | Author | Date |
|---|---|---|
| 7ee9782 | C-HW | 2023-07-13 |
MA plot
Enrichment analysis
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] pathview_1.38.0 org.Hs.eg.db_3.16.0
[3] AnnotationDbi_1.60.2 enrichplot_1.18.4
[5] clusterProfiler_4.6.2 reshape_0.8.9
[7] gridExtra_2.3 pheatmap_1.0.12
[9] SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0
[11] Biobase_2.58.0 GenomicRanges_1.50.2
[13] GenomeInfoDb_1.34.9 IRanges_2.32.0
[15] S4Vectors_0.36.2 BiocGenerics_0.44.0
[17] MatrixGenerics_1.10.0 matrixStats_1.0.0
[19] ggpubr_0.6.0 dplyr_1.1.2
[21] 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_1.5.0
[7] lazyeval_0.2.2 splines_4.2.2 BiocParallel_1.32.6
[10] digest_0.6.33 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] Biostrings_2.66.0 graphlayouts_1.0.0 colorspace_2.1-0
[22] blob_1.2.4 ggrepel_0.9.3 xfun_0.39
[25] crayon_1.5.2 RCurl_1.98-1.12 jsonlite_1.8.7
[28] graph_1.76.0 scatterpie_0.2.1 ape_5.7-1
[31] glue_1.6.2 polyclip_1.10-4 gtable_0.3.3
[34] zlibbioc_1.44.0 XVector_0.38.0 DelayedArray_0.24.0
[37] car_3.1-2 Rgraphviz_2.42.0 abind_1.4-5
[40] scales_1.2.1 DOSE_3.24.2 DBI_1.1.3
[43] rstatix_0.7.2 Rcpp_1.0.11 viridisLite_0.4.2
[46] gridGraphics_0.5-1 tidytree_0.4.4 bit_4.0.5
[49] httr_1.4.6 fgsea_1.24.0 RColorBrewer_1.1-3
[52] XML_3.99-0.14 pkgconfig_2.0.3 farver_2.1.1
[55] sass_0.4.7 utf8_1.2.3 labeling_0.4.2
[58] ggplotify_0.1.1 tidyselect_1.2.0 rlang_1.1.1
[61] reshape2_1.4.4 later_1.3.1 munsell_0.5.0
[64] tools_4.2.2 cachem_1.0.8 downloader_0.4
[67] cli_3.6.1 generics_0.1.3 RSQLite_2.3.1
[70] gson_0.1.0 broom_1.0.5 evaluate_0.21
[73] stringr_1.5.0 fastmap_1.1.1 yaml_2.3.7
[76] ggtree_3.6.2 knitr_1.43 bit64_4.0.5
[79] fs_1.6.3 tidygraph_1.2.3 purrr_1.0.1
[82] KEGGREST_1.38.0 ggraph_2.1.0 nlme_3.1-162
[85] whisker_0.4.1 KEGGgraph_1.58.3 aplot_0.1.10
[88] compiler_4.2.2 rstudioapi_0.15.0 png_0.1-8
[91] ggsignif_0.6.4 treeio_1.22.0 tibble_3.2.1
[94] tweenr_2.0.2 bslib_0.5.0 stringi_1.7.12
[97] highr_0.10 lattice_0.21-8 Matrix_1.5-4.1
[100] vctrs_0.6.3 pillar_1.9.0 lifecycle_1.0.3
[103] jquerylib_0.1.4 data.table_1.14.8 cowplot_1.1.1
[106] bitops_1.0-7 httpuv_1.6.11 patchwork_1.1.2
[109] qvalue_2.30.0 R6_2.5.1 promises_1.2.0.1
[112] codetools_0.2-19 MASS_7.3-60 rprojroot_2.0.3
[115] withr_2.5.0 GenomeInfoDbData_1.2.9 parallel_4.2.2
[118] grid_4.2.2 ggfun_0.1.1 tidyr_1.3.0
[121] HDO.db_0.99.1 rmarkdown_2.23 carData_3.0-5
[124] ggnewscale_0.4.9 git2r_0.32.0 ggforce_0.4.1