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regenerate these notebooks from command line, not knit, since that af…
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…fects the sessioninfo
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@sjspielman
sjspielman committed Nov 15, 2024
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87 changes: 44 additions & 43 deletions ...s-tumor-06/notebook/00-reference/00b_characterization_fetal_kidney_reference_Stewart.html
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Expand Up @@ -5510,8 +5510,9 @@ <h2>Base directories</h2>
</div>
<div id="input-files" class="section level2">
<h2>Input files</h2>
<p>The input file ../scratch/fetal_kidney.rds is the output of the
script <code>prepare-fetal-references.R</code>.</p>
<p>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 <code>prepare-fetal-references.R</code>.</p>
</div>
<div id="output-file" class="section level2">
<h2>Output file</h2>
Expand Down Expand Up @@ -5660,7 +5661,7 @@ <h2>Session info</h2>
## 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
Expand All @@ -5669,51 +5670,51 @@ <h2>Session info</h2>
## [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</code></pre>
## [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</code></pre>
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74 changes: 37 additions & 37 deletions .../cell-type-wilms-tumor-06/notebook/07_combined_annotation_across_samples_exploration.html
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Expand Up @@ -3534,7 +3534,7 @@ <h2>Session Info</h2>
## 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
Expand All @@ -3543,46 +3543,46 @@ <h2>Session Info</h2>
## [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</code></pre>
## [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</code></pre>
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