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allyhawkins committed Jan 15, 2025
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2 changes: 1 addition & 1 deletion analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.Rmd
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Expand Up @@ -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.
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54 changes: 32 additions & 22 deletions analyses/cell-type-ewings/exploratory_analysis/07-identify-max-rank-aucell.html
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Expand Up @@ -374,7 +374,8 @@ <h4 class="date">2025-01-15</h4>
<p>This notebook is used to find the appropriate <code>aucMaxRank</code>
to use with <code>AUCell</code> for all samples in
<code>SCPCP00015</code>.</p>
<p>From the <a href><code>AUCell</code> vignette</a>:</p>
<p>From the <a href="https://bioconductor.org/packages/release/bioc/vignettes/AUCell/inst/doc/AUCell.html"><code>AUCell</code>
vignette</a>:</p>
<blockquote>
<p>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
Expand Down Expand Up @@ -567,29 +568,38 @@ <h2>Session info</h2>
## [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</code></pre>
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