Group12_13
Chih-Hsuan Wu
Last updated: 2024-10-22
Checks: 7 0
Knit directory: DEanalysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2c1d57c | C-HW | 2024-10-22 | same criteria, FCcutoff 1.5 |
| html | 7bb637a | C-HW | 2024-10-21 | Build site. |
| html | c9a07f9 | C-HW | 2024-10-21 | Build site. |
| Rmd | f659575 | C-HW | 2024-10-21 | same DEG criteria for all methods |
| html | 28b9b7d | C-HW | 2024-10-14 | Build site. |
| Rmd | c4961dc | C-HW | 2024-10-14 | update Seurat result |
| html | 5e86686 | C-HW | 2023-12-15 | Build site. |
| Rmd | 036d5fc | C-HW | 2023-12-15 | wflow_publish(c("analysis/group12_13.Rmd", "analysis/group12_19.Rmd", |
| html | d7a7b73 | C-HW | 2023-12-10 | Build site. |
| Rmd | ae4b56c | C-HW | 2023-12-10 | adjust ylim of p-value histogram |
| html | ac027b0 | C-HW | 2023-12-09 | Build site. |
| Rmd | 582be29 | C-HW | 2023-12-09 | update new DE results |
| html | 2a17159 | C-HW | 2023-12-05 | Build site. |
| Rmd | e7f3de4 | C-HW | 2023-12-05 | fix Wilcox log2FC sign |
| html | e32516f | C-HW | 2023-12-05 | Build site. |
| html | bc13544 | C-HW | 2023-12-04 | Build site. |
| Rmd | 39196a3 | C-HW | 2023-12-04 | fix log2FC sign |
| html | 42900f0 | C-HW | 2023-12-01 | Build site. |
| Rmd | c774a2d | C-HW | 2023-12-01 | modify method title |
| Rmd | 031d955 | C-HW | 2023-12-01 | create t score comparison |
| html | 031d955 | C-HW | 2023-12-01 | create t score comparison |
| Rmd | 3803697 | C-HW | 2023-12-01 | upload rmd |
| html | 59b08c2 | C-HW | 2023-11-29 | update index, FD permuation, plots axes |
| html | e8b0519 | C-HW | 2023-11-29 | update all pairs |
| html | 6faf9c0 | C-HW | 2023-11-29 | group1213 |
| html | d7d838c | C-HW | 2023-08-11 | update graph |
| html | f314434 | C-HW | 2023-07-26 | add muscat methods |
| html | 7ee9782 | C-HW | 2023-07-13 | add 8_17 |
| html | ccb68e2 | C-HW | 2023-06-29 | log2fc consistence |
| html | 3121ffb | C-HW | 2023-06-22 | color palette heatmap |
| html | d8c99b1 | C-HW | 2023-06-16 | variation description |
| html | 366cd53 | C-HW | 2023-06-06 | add group8_17&2_19 |
| html | 95be122 | C-HW | 2023-05-25 | update 2_19 |
| html | 2107af3 | C-HW | 2023-05-24 | add methods_details |
| html | 13d726d | C-HW | 2023-05-18 | add DE results on different groups |
Data summary
Difference in library size
Asymptotic two-sample Kolmogorov-Smirnov test
data: subset(count_cell_df, Group == group1, totalcount)$totalcount and subset(count_cell_df, Group == group2, totalcount)$totalcount
D = 0.72806, p-value < 2.2e-16
alternative hypothesis: two-sided
Welch Two Sample t-test
data: subset(count_cell_df, Group == group1, totalcount)$totalcount and subset(count_cell_df, Group == group2, totalcount)$totalcount
t = 26.526, df = 513.08, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
665.3597 771.8005
sample estimates:
mean of x mean of y
2826.130 2107.549 Mean difference in raw data/normalized data
Number of DEGs from each method
Volcano plot
Histogram of p-value/adj.p-value
P-Value comparison across different methods
Log2 fold change comparison across different methods
Violin plot of log2mean of DEGs
Violin plot of gene expression frequency of DEGs
Upset plot
Heatmap of top DEGs
Poisson-glmm DEGs
UMI counts
VST data
CPM data
MA plot
Enrichment analysis
GO object
enrichKEGG object
| Version | Author | Date |
|---|---|---|
| 28b9b7d | C-HW | 2024-10-14 |
| 5e86686 | C-HW | 2023-12-15 |
| ac027b0 | C-HW | 2023-12-09 |
| 2a17159 | C-HW | 2023-12-05 |
| e32516f | C-HW | 2023-12-05 |
| bc13544 | C-HW | 2023-12-04 |
| 42900f0 | C-HW | 2023-12-01 |
| 031d955 | C-HW | 2023-12-01 |
| 59b08c2 | C-HW | 2023-11-29 |
| 6faf9c0 | C-HW | 2023-11-29 |
| d7d838c | C-HW | 2023-08-11 |
| 7ee9782 | C-HW | 2023-07-13 |
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Monterey 12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] UpSetR_1.4.0 SeuratObject_5.0.2
[3] sp_2.1-4 pathview_1.44.0
[5] org.Hs.eg.db_3.19.1 AnnotationDbi_1.66.0
[7] enrichplot_1.24.4 clusterProfiler_4.12.6
[9] reshape_0.8.9 gridExtra_2.3
[11] pheatmap_1.0.12 SingleCellExperiment_1.26.0
[13] SummarizedExperiment_1.34.0 Biobase_2.64.0
[15] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1
[17] IRanges_2.38.1 S4Vectors_0.42.1
[19] BiocGenerics_0.50.0 MatrixGenerics_1.16.0
[21] matrixStats_1.4.1 ggpubr_0.6.0
[23] dplyr_1.1.4 ggplot2_3.5.1
loaded via a namespace (and not attached):
[1] splines_4.4.1 later_1.3.2 bitops_1.0-9
[4] ggplotify_0.1.2 tibble_3.2.1 R.oo_1.26.0
[7] polyclip_1.10-7 graph_1.82.0 XML_3.99-0.17
[10] lifecycle_1.0.4 httr2_1.0.5 rstatix_0.7.2
[13] rprojroot_2.0.4 globals_0.16.3 lattice_0.22-6
[16] MASS_7.3-61 backports_1.5.0 magrittr_2.0.3
[19] sass_0.4.9 rmarkdown_2.28 jquerylib_0.1.4
[22] yaml_2.3.10 httpuv_1.6.15 spam_2.11-0
[25] cowplot_1.1.3 DBI_1.2.3 RColorBrewer_1.1-3
[28] abind_1.4-8 zlibbioc_1.50.0 purrr_1.0.2
[31] R.utils_2.12.3 ggraph_2.2.1 RCurl_1.98-1.16
[34] yulab.utils_0.1.7 tweenr_2.0.3 rappdirs_0.3.3
[37] git2r_0.35.0 GenomeInfoDbData_1.2.12 ggrepel_0.9.6
[40] listenv_0.9.1 tidytree_0.4.6 parallelly_1.38.0
[43] codetools_0.2-20 DelayedArray_0.30.1 DOSE_3.30.5
[46] ggforce_0.4.2 tidyselect_1.2.1 aplot_0.2.3
[49] UCSC.utils_1.0.0 farver_2.1.2 viridis_0.6.5
[52] jsonlite_1.8.9 progressr_0.14.0 tidygraph_1.3.1
[55] Formula_1.2-5 ggnewscale_0.5.0 tools_4.4.1
[58] treeio_1.28.0 Rcpp_1.0.13 glue_1.8.0
[61] SparseArray_1.4.8 xfun_0.48 qvalue_2.36.0
[64] withr_3.0.1 fastmap_1.2.0 fansi_1.0.6
[67] digest_0.6.37 R6_2.5.1 gridGraphics_0.5-1
[70] colorspace_2.1-1 GO.db_3.19.1 RSQLite_2.3.7
[73] R.methodsS3_1.8.2 utf8_1.2.4 tidyr_1.3.1
[76] generics_0.1.3 data.table_1.16.2 graphlayouts_1.2.0
[79] httr_1.4.7 S4Arrays_1.4.1 scatterpie_0.2.4
[82] whisker_0.4.1 pkgconfig_2.0.3 gtable_0.3.5
[85] blob_1.2.4 workflowr_1.7.1 XVector_0.44.0
[88] shadowtext_0.1.4 htmltools_0.5.8.1 carData_3.0-5
[91] dotCall64_1.2 fgsea_1.30.0 scales_1.3.0
[94] png_0.1-8 ggfun_0.1.6 knitr_1.48
[97] rstudioapi_0.17.0 reshape2_1.4.4 nlme_3.1-166
[100] cachem_1.1.0 stringr_1.5.1 parallel_4.4.1
[103] pillar_1.9.0 grid_4.4.1 vctrs_0.6.5
[106] promises_1.3.0 car_3.1-3 Rgraphviz_2.48.0
[109] evaluate_1.0.1 KEGGgraph_1.64.0 cli_3.6.3
[112] compiler_4.4.1 rlang_1.1.4 crayon_1.5.3
[115] future.apply_1.11.2 ggsignif_0.6.4 labeling_0.4.3
[118] plyr_1.8.9 fs_1.6.4 stringi_1.8.4
[121] viridisLite_0.4.2 BiocParallel_1.38.0 munsell_0.5.1
[124] Biostrings_2.72.1 lazyeval_0.2.2 GOSemSim_2.30.2
[127] Matrix_1.7-1 patchwork_1.3.0 bit64_4.5.2
[130] future_1.34.0 KEGGREST_1.44.1 highr_0.11
[133] igraph_2.1.1 broom_1.0.7 memoise_2.0.1
[136] bslib_0.8.0 ggtree_3.12.0 fastmatch_1.1-4
[139] bit_4.5.0 ape_5.8 gson_0.1.0