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differences for PR #117
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26 changes: 13 additions & 13 deletions 03-import-annotate.md
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Expand Up @@ -780,22 +780,22 @@ other attached packages:
[7] MatrixGenerics_1.16.0 matrixStats_1.4.1
[9] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1
[11] IRanges_2.38.1 S4Vectors_0.42.1
[13] BiocGenerics_0.50.0 knitr_1.48
[13] BiocGenerics_0.50.0 knitr_1.49
loaded via a namespace (and not attached):
[1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9
[4] highr_0.11 compiler_4.4.2 BiocManager_1.30.25
[7] renv_1.0.11 crayon_1.5.3 blob_1.2.4
[10] Biostrings_2.72.1 png_0.1-8 fastmap_1.2.0
[13] yaml_2.3.10 lattice_0.22-6 R6_2.5.1
[16] XVector_0.44.0 S4Arrays_1.4.1 DelayedArray_0.30.1
[19] GenomeInfoDbData_1.2.12 DBI_1.2.3 rlang_1.1.4
[22] KEGGREST_1.44.1 cachem_1.1.0 xfun_0.49
[25] bit64_4.5.2 memoise_2.0.1 SparseArray_1.4.8
[28] RSQLite_2.3.7 cli_3.6.3 zlibbioc_1.50.0
[31] grid_4.4.2 vctrs_0.6.5 evaluate_1.0.1
[34] abind_1.4-8 httr_1.4.7 pkgconfig_2.0.3
[37] tools_4.4.2 UCSC.utils_1.0.0
[4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11
[7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1
[10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10
[13] lattice_0.22-6 R6_2.5.1 XVector_0.44.0
[16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12
[19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1
[22] cachem_1.1.0 xfun_0.49 bit64_4.5.2
[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8
[28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2
[31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8
[34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2
[37] UCSC.utils_1.0.0
```

::: keypoints
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54 changes: 27 additions & 27 deletions 04-exploratory-qc.md
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Expand Up @@ -449,7 +449,7 @@ attached base packages:
other attached packages:
[1] iSEE_2.16.0 SingleCellExperiment_1.26.0
[3] hexbin_1.28.4 RColorBrewer_1.1-3
[3] hexbin_1.28.5 RColorBrewer_1.1-3
[5] ComplexHeatmap_2.20.0 ggplot2_3.5.1
[7] vsn_3.72.0 DESeq2_1.44.0
[9] SummarizedExperiment_1.34.0 Biobase_2.64.0
Expand All @@ -460,37 +460,37 @@ other attached packages:
loaded via a namespace (and not attached):
[1] rlang_1.1.4 magrittr_2.0.3 shinydashboard_0.7.2
[4] clue_0.3-65 GetoptLong_1.0.5 compiler_4.4.2
[4] clue_0.3-66 GetoptLong_1.0.5 compiler_4.4.2
[7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5
[10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3
[16] utf8_1.2.4 promises_1.3.0 shinyAce_0.4.3
[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3
[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49
[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9
[25] listviewer_4.0.0 highr_0.11 later_1.3.2
[28] DelayedArray_0.30.1 BiocParallel_1.38.0 parallel_4.4.2
[31] cluster_2.1.6 R6_2.5.1 bslib_0.8.0
[34] limma_3.60.6 jquerylib_0.1.4 Rcpp_1.0.13-1
[37] iterators_1.0.14 knitr_1.48 httpuv_1.6.15
[40] Matrix_1.7-1 splines_4.4.2 igraph_2.1.1
[43] tidyselect_1.2.1 abind_1.4-8 yaml_2.3.10
[46] doParallel_1.0.17 codetools_0.2-20 affy_1.82.0
[49] miniUI_0.1.1.1 lattice_0.22-6 tibble_3.2.1
[52] shiny_1.9.1 withr_3.0.2 evaluate_1.0.1
[55] circlize_0.4.16 pillar_1.9.0 affyio_1.74.0
[58] BiocManager_1.30.25 renv_1.0.11 DT_0.33
[61] foreach_1.5.2 shinyjs_2.1.0 generics_0.1.3
[64] munsell_0.5.1 scales_1.3.0 xtable_1.8-4
[67] glue_1.8.0 tools_4.4.2 colourpicker_1.3.0
[70] locfit_1.5-9.10 colorspace_2.1-1 nlme_3.1-166
[73] GenomeInfoDbData_1.2.12 vipor_0.4.7 cli_3.6.3
[76] fansi_1.0.6 viridisLite_0.4.2 S4Arrays_1.4.1
[79] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4
[82] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8
[85] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23
[88] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4
[91] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2
[94] statmod_1.5.0 mime_0.12
[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1
[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6
[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6
[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14
[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1
[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1
[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17
[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1
[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1
[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16
[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25
[58] renv_1.0.11 DT_0.33 foreach_1.5.2
[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1
[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0
[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10
[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12
[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6
[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4
[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9
[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6
[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4
[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7
[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0
[94] mime_0.12
```

:::::::::::::::::::::::::::::::::::::::: keypoints
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34 changes: 17 additions & 17 deletions 07-gene-set-analysis.md
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Expand Up @@ -500,9 +500,9 @@ microbenchmark(

``` output
Unit: microseconds
expr min lq mean median uq max neval
fisher 244.097 247.938 256.9654 250.769 257.2005 457.986 100
hyper 1.472 1.673 2.4975 2.394 2.8960 19.216 100
expr min lq mean median uq max neval
fisher 244.647 248.519 268.42240 251.5640 260.3360 1475.363 100
hyper 1.432 1.638 2.29862 1.9735 2.8855 6.071 100
```

It is very astonishing that `phyper()` is hundreds of times faster than
Expand Down Expand Up @@ -1230,7 +1230,7 @@ resTimeGO = enrichGO(gene = timeDEgenes,
```

``` output
--> Expected input gene ID: 22026,381760,114662,54388,21857,53419
--> Expected input gene ID: 113002583,66233,18783,12846,26927,433700
```

``` output
Expand Down Expand Up @@ -1478,19 +1478,19 @@ mmu00592 alpha-Linolenic acid metabolism - Mus mus
mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse)
mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
mmu00590 16/460 89/9808 0.1797753 3.833122 5.955759 3.144974e-06
mmu00591 12/460 55/9808 0.2181818 4.652016 6.024660 6.826961e-06
mmu00565 11/460 48/9808 0.2291667 4.886232 5.987039 1.000946e-05
mmu00592 8/460 25/9808 0.3200000 6.822957 6.466439 1.175542e-05
mmu04913 12/460 64/9808 0.1875000 3.997826 5.337224 3.479789e-05
mmu04061 14/460 95/9808 0.1473684 3.142151 4.653962 1.272854e-04
p.adjust qvalue
mmu00590 0.0009139838 0.000791944
mmu00591 0.0009139838 0.000791944
mmu00565 0.0009139838 0.000791944
mmu00592 0.0009139838 0.000791944
mmu04913 0.0021644287 0.001875423
mmu04061 0.0065976247 0.005716676
mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06
mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06
mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06
mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05
mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05
mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04
p.adjust qvalue
mmu00590 0.0009101439 0.0007860892
mmu00591 0.0009101439 0.0007860892
mmu00565 0.0009101439 0.0007860892
mmu00592 0.0009101439 0.0007860892
mmu04913 0.0021499443 0.0018569019
mmu04061 0.0065486813 0.0056560810
geneID
mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687
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86 changes: 0 additions & 86 deletions config.yaml
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36 changes: 18 additions & 18 deletions md5sum.txt
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@@ -1,19 +1,19 @@
"file" "checksum" "built" "date"
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