diff --git a/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.Rmd b/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.Rmd index 9de965788..6e97f5bbe 100644 --- a/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.Rmd +++ b/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.Rmd @@ -10,7 +10,7 @@ output: This notebook is used to find the appropriate `aucMaxRank` to use with `AUCell` for all samples in `SCPCP00015`. -From the [`AUCell` vignette](): +From the [`AUCell` vignette](https://bioconductor.org/packages/release/bioc/vignettes/AUCell/inst/doc/AUCell.html): > It is important to check that most cells have at least the number of expressed/detected genes that are going to be used to calculate the AUC (aucMaxRank in calcAUC()). The histogram provided by AUCell_buildRankings() allows to quickly check this distribution. diff --git a/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.html b/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.html index ba9e1408f..ac3c9733e 100644 --- a/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.html +++ b/analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.html @@ -374,7 +374,8 @@

2025-01-15

This notebook is used to find the appropriate aucMaxRank to use with AUCell for all samples in SCPCP00015.

-

From the AUCell vignette:

+

From the AUCell +vignette:

It is important to check that most cells have at least the number of expressed/detected genes that are going to be used to calculate the AUC @@ -567,29 +568,38 @@

Session info

## [1] stats4 stats graphics grDevices datasets utils methods base ## ## other attached packages: -## [1] ggplot2_3.5.1 SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 Biobase_2.64.0 GenomicRanges_1.56.1 -## [6] GenomeInfoDb_1.40.1 IRanges_2.38.1 S4Vectors_0.42.1 BiocGenerics_0.50.0 MatrixGenerics_1.16.0 -## [11] matrixStats_1.3.0 +## [1] ggplot2_3.5.1 SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 Biobase_2.64.0 +## [5] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 IRanges_2.38.1 S4Vectors_0.42.1 +## [9] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 matrixStats_1.3.0 ## ## loaded via a namespace (and not attached): -## [1] DBI_1.2.3 GSEABase_1.66.0 rlang_1.1.4 magrittr_2.0.3 clue_0.3-65 GetoptLong_1.0.5 -## [7] AUCell_1.26.0 RSQLite_2.3.7 compiler_4.4.2 DelayedMatrixStats_1.26.0 png_0.1-8 vctrs_0.6.5 -## [13] stringr_1.5.1 pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3 fastmap_1.2.0 XVector_0.44.0 -## [19] scuttle_1.14.0 labeling_0.4.3 utf8_1.2.4 rmarkdown_2.27 tzdb_0.4.0 graph_1.82.0 -## [25] UCSC.utils_1.0.0 purrr_1.0.2 bit_4.0.5 xfun_0.46 bluster_1.14.0 zlibbioc_1.50.0 -## [31] cachem_1.1.0 beachmat_2.20.0 jsonlite_1.8.8 blob_1.2.4 highr_0.11 DelayedArray_0.30.1 -## [37] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6 R6_2.5.1 bslib_0.8.0 stringi_1.8.4 -## [43] RColorBrewer_1.1-3 jquerylib_0.1.4 Rcpp_1.0.13 iterators_1.0.14 knitr_1.48 R.utils_2.12.3 -## [49] readr_2.1.5 Matrix_1.7-0 igraph_2.0.3 tidyselect_1.2.1 abind_1.4-5 yaml_2.3.10 -## [55] doParallel_1.0.17 codetools_0.2-20 lattice_0.22-6 tibble_3.2.1 KEGGREST_1.44.1 withr_3.0.0 -## [61] evaluate_0.24.0 Biostrings_2.72.1 circlize_0.4.16 pillar_1.9.0 BiocManager_1.30.23 renv_1.0.7 -## [67] foreach_1.5.2 generics_0.1.3 vroom_1.6.5 rprojroot_2.0.4 hms_1.1.3 sparseMatrixStats_1.16.0 -## [73] munsell_0.5.1 scales_1.3.0 xtable_1.8-4 glue_1.7.0 tools_4.4.2 data.table_1.15.4 -## [79] BiocNeighbors_1.22.0 annotate_1.82.0 forcats_1.0.0 XML_3.99-0.17 fs_1.6.4 grid_4.4.2 -## [85] tidyr_1.3.1 AnnotationDbi_1.66.0 colorspace_2.1-1 GenomeInfoDbData_1.2.12 patchwork_1.2.0 cli_3.6.3 -## [91] fansi_1.0.6 S4Arrays_1.4.1 viridisLite_0.4.2 ComplexHeatmap_2.20.0 dplyr_1.1.4 gtable_0.3.5 -## [97] R.methodsS3_1.8.2 sass_0.4.9 digest_0.6.36 SparseArray_1.4.8 rjson_0.2.21 farver_2.1.2 -## [103] R.oo_1.26.0 memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 GlobalOptions_0.1.2 +## [1] DBI_1.2.3 GSEABase_1.66.0 rlang_1.1.4 magrittr_2.0.3 +## [5] clue_0.3-65 GetoptLong_1.0.5 AUCell_1.26.0 RSQLite_2.3.7 +## [9] compiler_4.4.2 DelayedMatrixStats_1.26.0 png_0.1-8 vctrs_0.6.5 +## [13] stringr_1.5.1 pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3 +## [17] fastmap_1.2.0 XVector_0.44.0 scuttle_1.14.0 labeling_0.4.3 +## [21] utf8_1.2.4 rmarkdown_2.27 tzdb_0.4.0 graph_1.82.0 +## [25] UCSC.utils_1.0.0 purrr_1.0.2 bit_4.0.5 xfun_0.46 +## [29] bluster_1.14.0 zlibbioc_1.50.0 cachem_1.1.0 beachmat_2.20.0 +## [33] jsonlite_1.8.8 blob_1.2.4 highr_0.11 DelayedArray_0.30.1 +## [37] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6 R6_2.5.1 +## [41] bslib_0.8.0 stringi_1.8.4 RColorBrewer_1.1-3 jquerylib_0.1.4 +## [45] Rcpp_1.0.13 iterators_1.0.14 knitr_1.48 R.utils_2.12.3 +## [49] readr_2.1.5 Matrix_1.7-0 igraph_2.0.3 tidyselect_1.2.1 +## [53] abind_1.4-5 yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20 +## [57] lattice_0.22-6 tibble_3.2.1 KEGGREST_1.44.1 withr_3.0.0 +## [61] evaluate_0.24.0 Biostrings_2.72.1 circlize_0.4.16 pillar_1.9.0 +## [65] BiocManager_1.30.23 renv_1.0.7 foreach_1.5.2 generics_0.1.3 +## [69] vroom_1.6.5 rprojroot_2.0.4 hms_1.1.3 sparseMatrixStats_1.16.0 +## [73] munsell_0.5.1 scales_1.3.0 xtable_1.8-4 glue_1.7.0 +## [77] tools_4.4.2 data.table_1.15.4 BiocNeighbors_1.22.0 annotate_1.82.0 +## [81] forcats_1.0.0 XML_3.99-0.17 fs_1.6.4 grid_4.4.2 +## [85] tidyr_1.3.1 AnnotationDbi_1.66.0 colorspace_2.1-1 GenomeInfoDbData_1.2.12 +## [89] patchwork_1.2.0 cli_3.6.3 fansi_1.0.6 S4Arrays_1.4.1 +## [93] viridisLite_0.4.2 ComplexHeatmap_2.20.0 dplyr_1.1.4 gtable_0.3.5 +## [97] R.methodsS3_1.8.2 sass_0.4.9 digest_0.6.36 SparseArray_1.4.8 +## [101] rjson_0.2.21 farver_2.1.2 R.oo_1.26.0 memoise_2.0.1 +## [105] htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 GlobalOptions_0.1.2 ## [109] bit64_4.0.5