diff --git a/analyses/cell-type-wilms-tumor-06/notebook/00-reference/00b_characterization_fetal_kidney_reference_Stewart.html b/analyses/cell-type-wilms-tumor-06/notebook/00-reference/00b_characterization_fetal_kidney_reference_Stewart.html index 133065876..15a769467 100644 --- a/analyses/cell-type-wilms-tumor-06/notebook/00-reference/00b_characterization_fetal_kidney_reference_Stewart.html +++ b/analyses/cell-type-wilms-tumor-06/notebook/00-reference/00b_characterization_fetal_kidney_reference_Stewart.html @@ -5510,8 +5510,9 @@

Base directories

Input files

-

The input file ../scratch/fetal_kidney.rds is the output of the -script prepare-fetal-references.R.

+

The input file +/Users/sjspielman/ALSF/open-scpca/OpenScPCA-analysis/analyses/cell-type-wilms-tumor-06/scratch/fetal_kidney.rds +is the output of the script prepare-fetal-references.R.

Output file

@@ -5660,7 +5661,7 @@

Session info

## tzcode source: internal ## ## attached base packages: -## [1] stats graphics grDevices utils datasets methods base +## [1] stats graphics grDevices datasets utils methods base ## ## other attached packages: ## [1] patchwork_1.2.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 @@ -5669,51 +5670,51 @@

Session info

## [13] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 ## ## loaded via a namespace (and not attached): -## [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 -## [4] magrittr_2.0.3 spatstat.utils_3.1-0 farver_2.1.2 -## [7] rmarkdown_2.28 DElegate_1.2.1 fs_1.6.4 -## [10] vctrs_0.6.5 ROCR_1.0-11 spatstat.explore_3.3-2 -## [13] htmltools_0.5.8.1 gridGraphics_0.5-1 sass_0.4.9 -## [16] sctransform_0.4.1 parallelly_1.38.0 KernSmooth_2.23-24 -## [19] bslib_0.8.0 htmlwidgets_1.6.4 ica_1.0-3 -## [22] plyr_1.8.9 plotly_4.10.4 zoo_1.8-12 -## [25] cachem_1.1.0 igraph_2.0.3 mime_0.12 -## [28] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-0 -## [31] R6_2.5.1 fastmap_1.2.0 MatrixGenerics_1.16.0 -## [34] fitdistrplus_1.2-1 future_1.34.0 shiny_1.9.1 -## [37] digest_0.6.37 colorspace_2.1-1 rprojroot_2.0.4 -## [40] tensor_1.5 RSpectra_0.16-2 irlba_2.3.5.1 -## [43] crosstalk_1.2.1 labeling_0.4.3 progressr_0.14.0 -## [46] fansi_1.0.6 spatstat.sparse_3.1-0 timechange_0.3.0 -## [49] httr_1.4.7 polyclip_1.10-7 abind_1.4-5 -## [52] compiler_4.4.0 bit64_4.0.5 withr_3.0.1 -## [55] viridis_0.6.5 fastDummies_1.7.4 highr_0.11 -## [58] MASS_7.3-61 tools_4.4.0 lmtest_0.9-40 -## [61] httpuv_1.6.15 future.apply_1.11.2 goftest_1.2-3 -## [64] glue_1.7.0 nlme_3.1-166 promises_1.3.0 -## [67] grid_4.4.0 Rtsne_0.17 cluster_2.1.6 -## [70] reshape2_1.4.4 generics_0.1.3 gtable_0.3.5 -## [73] spatstat.data_3.1-2 tzdb_0.4.0 data.table_1.16.0 -## [76] hms_1.1.3 utf8_1.2.4 spatstat.geom_3.3-2 -## [79] RcppAnnoy_0.0.22 ggrepel_0.9.5 RANN_2.6.2 -## [82] pillar_1.9.0 vroom_1.6.5 limma_3.60.4 -## [85] yulab.utils_0.1.7 spam_2.10-0 RcppHNSW_0.6.0 -## [88] later_1.3.2 splines_4.4.0 lattice_0.22-6 -## [91] bit_4.0.5 survival_3.7-0 deldir_2.0-4 +## [1] RColorBrewer_1.1-3 jsonlite_1.8.8 magrittr_2.0.3 +## [4] spatstat.utils_3.1-0 farver_2.1.2 rmarkdown_2.28 +## [7] DElegate_1.2.1 fs_1.6.4 vctrs_0.6.5 +## [10] ROCR_1.0-11 spatstat.explore_3.3-2 htmltools_0.5.8.1 +## [13] gridGraphics_0.5-1 sass_0.4.9 sctransform_0.4.1 +## [16] parallelly_1.38.0 KernSmooth_2.23-24 bslib_0.8.0 +## [19] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9 +## [22] plotly_4.10.4 zoo_1.8-12 cachem_1.1.0 +## [25] igraph_2.0.3 mime_0.12 lifecycle_1.0.4 +## [28] pkgconfig_2.0.3 Matrix_1.7-0 R6_2.5.1 +## [31] fastmap_1.2.0 MatrixGenerics_1.16.0 fitdistrplus_1.2-1 +## [34] future_1.34.0 shiny_1.9.1 digest_0.6.37 +## [37] colorspace_2.1-1 rprojroot_2.0.4 tensor_1.5 +## [40] RSpectra_0.16-2 irlba_2.3.5.1 crosstalk_1.2.1 +## [43] labeling_0.4.3 progressr_0.14.0 timechange_0.3.0 +## [46] fansi_1.0.6 spatstat.sparse_3.1-0 httr_1.4.7 +## [49] polyclip_1.10-7 abind_1.4-5 compiler_4.4.0 +## [52] bit64_4.0.5 withr_3.0.1 viridis_0.6.5 +## [55] fastDummies_1.7.4 highr_0.11 MASS_7.3-61 +## [58] tools_4.4.0 lmtest_0.9-40 httpuv_1.6.15 +## [61] future.apply_1.11.2 goftest_1.2-3 glue_1.7.0 +## [64] nlme_3.1-166 promises_1.3.0 grid_4.4.0 +## [67] Rtsne_0.17 cluster_2.1.6 reshape2_1.4.4 +## [70] generics_0.1.3 gtable_0.3.5 spatstat.data_3.1-2 +## [73] tzdb_0.4.0 data.table_1.16.0 hms_1.1.3 +## [76] utf8_1.2.4 spatstat.geom_3.3-2 RcppAnnoy_0.0.22 +## [79] ggrepel_0.9.5 RANN_2.6.2 pillar_1.9.0 +## [82] vroom_1.6.5 limma_3.60.4 yulab.utils_0.1.7 +## [85] spam_2.10-0 RcppHNSW_0.6.0 later_1.3.2 +## [88] splines_4.4.0 lattice_0.22-6 bit_4.0.5 +## [91] renv_1.0.7 survival_3.7-0 deldir_2.0-4 ## [94] tidyselect_1.2.1 locfit_1.5-9.10 miniUI_0.1.1.1 ## [97] pbapply_1.7-2 knitr_1.48 gridExtra_2.3 ## [100] edgeR_4.2.1 scattermore_1.2 xfun_0.47 ## [103] statmod_1.5.0 matrixStats_1.3.0 DT_0.33 ## [106] stringi_1.8.4 lazyeval_0.2.2 yaml_2.3.10 -## [109] evaluate_0.24.0 codetools_0.2-20 ggplotify_0.1.2 -## [112] cli_3.6.3 uwot_0.2.2 xtable_1.8-4 -## [115] reticulate_1.38.0 munsell_0.5.1 jquerylib_0.1.4 -## [118] Rcpp_1.0.13 globals_0.16.3 spatstat.random_3.3-1 -## [121] png_0.1-8 spatstat.univar_3.0-0 parallel_4.4.0 -## [124] assertthat_0.2.1 dotCall64_1.1-1 sparseMatrixStats_1.16.0 -## [127] listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0 -## [130] ggridges_0.5.6 crayon_1.5.3 leiden_0.4.3.1 -## [133] rlang_1.1.4 cowplot_1.1.3 +## [109] evaluate_0.24.0 codetools_0.2-20 BiocManager_1.30.25 +## [112] ggplotify_0.1.2 cli_3.6.3 uwot_0.2.2 +## [115] xtable_1.8-4 reticulate_1.38.0 munsell_0.5.1 +## [118] jquerylib_0.1.4 Rcpp_1.0.13 globals_0.16.3 +## [121] spatstat.random_3.3-1 png_0.1-8 spatstat.univar_3.0-0 +## [124] parallel_4.4.0 assertthat_0.2.1 dotCall64_1.1-1 +## [127] sparseMatrixStats_1.16.0 listenv_0.9.1 viridisLite_0.4.2 +## [130] scales_1.3.0 ggridges_0.5.6 crayon_1.5.3 +## [133] leiden_0.4.3.1 rlang_1.1.4 cowplot_1.1.3
diff --git a/analyses/cell-type-wilms-tumor-06/notebook/07_combined_annotation_across_samples_exploration.html b/analyses/cell-type-wilms-tumor-06/notebook/07_combined_annotation_across_samples_exploration.html index d6be8e8aa..80fec741e 100644 --- a/analyses/cell-type-wilms-tumor-06/notebook/07_combined_annotation_across_samples_exploration.html +++ b/analyses/cell-type-wilms-tumor-06/notebook/07_combined_annotation_across_samples_exploration.html @@ -3534,7 +3534,7 @@

Session Info

## tzcode source: internal ## ## attached base packages: -## [1] stats graphics grDevices utils datasets methods base +## [1] stats graphics grDevices datasets utils methods base ## ## other attached packages: ## [1] DT_0.33 patchwork_1.2.0 lubridate_1.9.3 forcats_1.0.0 @@ -3543,46 +3543,46 @@

Session Info

## [13] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 ## ## loaded via a namespace (and not attached): -## [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 -## [4] magrittr_2.0.3 spatstat.utils_3.1-0 farver_2.1.2 -## [7] rmarkdown_2.28 vctrs_0.6.5 ROCR_1.0-11 -## [10] spatstat.explore_3.3-2 htmltools_0.5.8.1 sass_0.4.9 -## [13] sctransform_0.4.1 parallelly_1.38.0 KernSmooth_2.23-24 -## [16] bslib_0.8.0 htmlwidgets_1.6.4 ica_1.0-3 -## [19] plyr_1.8.9 plotly_4.10.4 zoo_1.8-12 -## [22] cachem_1.1.0 igraph_2.0.3 mime_0.12 -## [25] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-0 -## [28] R6_2.5.1 fastmap_1.2.0 fitdistrplus_1.2-1 -## [31] future_1.34.0 shiny_1.9.1 digest_0.6.37 -## [34] colorspace_2.1-1 rprojroot_2.0.4 tensor_1.5 -## [37] RSpectra_0.16-2 irlba_2.3.5.1 labeling_0.4.3 -## [40] progressr_0.14.0 fansi_1.0.6 spatstat.sparse_3.1-0 -## [43] timechange_0.3.0 httr_1.4.7 polyclip_1.10-7 -## [46] abind_1.4-5 compiler_4.4.0 bit64_4.0.5 -## [49] withr_3.0.1 fastDummies_1.7.4 highr_0.11 -## [52] MASS_7.3-61 tools_4.4.0 lmtest_0.9-40 -## [55] httpuv_1.6.15 future.apply_1.11.2 goftest_1.2-3 -## [58] glue_1.7.0 nlme_3.1-166 promises_1.3.0 -## [61] grid_4.4.0 Rtsne_0.17 cluster_2.1.6 -## [64] reshape2_1.4.4 generics_0.1.3 gtable_0.3.5 -## [67] spatstat.data_3.1-2 tzdb_0.4.0 data.table_1.16.0 -## [70] hms_1.1.3 utf8_1.2.4 spatstat.geom_3.3-2 -## [73] RcppAnnoy_0.0.22 ggrepel_0.9.5 RANN_2.6.2 -## [76] pillar_1.9.0 vroom_1.6.5 spam_2.10-0 -## [79] RcppHNSW_0.6.0 later_1.3.2 splines_4.4.0 -## [82] lattice_0.22-6 bit_4.0.5 survival_3.7-0 +## [1] RColorBrewer_1.1-3 jsonlite_1.8.8 magrittr_2.0.3 +## [4] spatstat.utils_3.1-0 farver_2.1.2 rmarkdown_2.28 +## [7] vctrs_0.6.5 ROCR_1.0-11 spatstat.explore_3.3-2 +## [10] htmltools_0.5.8.1 sass_0.4.9 sctransform_0.4.1 +## [13] parallelly_1.38.0 KernSmooth_2.23-24 bslib_0.8.0 +## [16] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9 +## [19] plotly_4.10.4 zoo_1.8-12 cachem_1.1.0 +## [22] igraph_2.0.3 mime_0.12 lifecycle_1.0.4 +## [25] pkgconfig_2.0.3 Matrix_1.7-0 R6_2.5.1 +## [28] fastmap_1.2.0 fitdistrplus_1.2-1 future_1.34.0 +## [31] shiny_1.9.1 digest_0.6.37 colorspace_2.1-1 +## [34] rprojroot_2.0.4 tensor_1.5 RSpectra_0.16-2 +## [37] irlba_2.3.5.1 labeling_0.4.3 progressr_0.14.0 +## [40] fansi_1.0.6 spatstat.sparse_3.1-0 timechange_0.3.0 +## [43] httr_1.4.7 polyclip_1.10-7 abind_1.4-5 +## [46] compiler_4.4.0 bit64_4.0.5 withr_3.0.1 +## [49] fastDummies_1.7.4 highr_0.11 MASS_7.3-61 +## [52] tools_4.4.0 lmtest_0.9-40 httpuv_1.6.15 +## [55] future.apply_1.11.2 goftest_1.2-3 glue_1.7.0 +## [58] nlme_3.1-166 promises_1.3.0 grid_4.4.0 +## [61] Rtsne_0.17 cluster_2.1.6 reshape2_1.4.4 +## [64] generics_0.1.3 gtable_0.3.5 spatstat.data_3.1-2 +## [67] tzdb_0.4.0 data.table_1.16.0 hms_1.1.3 +## [70] utf8_1.2.4 spatstat.geom_3.3-2 RcppAnnoy_0.0.22 +## [73] ggrepel_0.9.5 RANN_2.6.2 pillar_1.9.0 +## [76] vroom_1.6.5 spam_2.10-0 RcppHNSW_0.6.0 +## [79] later_1.3.2 splines_4.4.0 lattice_0.22-6 +## [82] bit_4.0.5 renv_1.0.7 survival_3.7-0 ## [85] deldir_2.0-4 tidyselect_1.2.1 miniUI_0.1.1.1 ## [88] pbapply_1.7-2 knitr_1.48 gridExtra_2.3 ## [91] scattermore_1.2 xfun_0.47 matrixStats_1.3.0 ## [94] stringi_1.8.4 lazyeval_0.2.2 yaml_2.3.10 -## [97] evaluate_0.24.0 codetools_0.2-20 cli_3.6.3 -## [100] uwot_0.2.2 xtable_1.8-4 reticulate_1.38.0 -## [103] munsell_0.5.1 jquerylib_0.1.4 Rcpp_1.0.13 -## [106] globals_0.16.3 spatstat.random_3.3-1 png_0.1-8 -## [109] spatstat.univar_3.0-0 parallel_4.4.0 dotCall64_1.1-1 -## [112] listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0 -## [115] ggridges_0.5.6 crayon_1.5.3 leiden_0.4.3.1 -## [118] rlang_1.1.4 cowplot_1.1.3 +## [97] evaluate_0.24.0 codetools_0.2-20 BiocManager_1.30.25 +## [100] cli_3.6.3 uwot_0.2.2 xtable_1.8-4 +## [103] reticulate_1.38.0 munsell_0.5.1 jquerylib_0.1.4 +## [106] Rcpp_1.0.13 globals_0.16.3 spatstat.random_3.3-1 +## [109] png_0.1-8 spatstat.univar_3.0-0 parallel_4.4.0 +## [112] dotCall64_1.1-1 listenv_0.9.1 viridisLite_0.4.2 +## [115] scales_1.3.0 ggridges_0.5.6 crayon_1.5.3 +## [118] leiden_0.4.3.1 rlang_1.1.4 cowplot_1.1.3