Note: some texts in this report are based on the book Orchestrating Single-Cell Analysis with Bioconductor published under CC BY 4.0


Project: PBMC 1k

1000 peripheral blood mononuclear cells by 10x Genomics

markers_cluster_graph_louvain_r0.4

Dimred plots

UMAP

PCA

Results by levels

1

2

3

4

5

6

7

Results by test type

binom

t

wilcox

markers_cluster_graph_louvain_r0.8_phase_block

Dimred plots

UMAP

Results by levels

1

10

2

3

4

5

6

7

8

9

Results by test type

binom

t

wilcox

Show used functions ▾

Show input parameters

Main config

## $PROJECT_NAME
## [1] "PBMC 1k"
## 
## $PROJECT_DESCRIPTION
## [1] "1000 peripheral blood mononuclear cells by 10x Genomics"
## 
## $INSTITUTE
## [1] "Example institute"
## 
## $LABORATORY
## [1] "Example laboratory"
## 
## $PEOPLE
## [1] "Example person 1, Example person 2"
## 
## $ORGANISM
## [1] "human"
## 
## $ANNOTATION_LIST
## $ANNOTATION_LIST$human
## [1] "org.Hs.eg.db"
## 
## $ANNOTATION_LIST$mouse
## [1] "org.Mm.eg.db"
## 
## 
## $ENSEMBL_SPECIES
## [1] "Homo_sapiens"
## 
## $CSS_FILE
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/Rmd/common/stylesheet.css"
## 
## $BASE_OUT_DIR
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/output"
## 
## $ANNOTATION_DB_FILE
## [1] "/usr/local/lib/R/site-library/org.Hs.eg.db/extdata/org.Hs.eg.sqlite"
## 
## $ANNOTATION_PKG
## [1] "org.Hs.eg.db"
## 
## attr(,"class")
## [1] "scdrake_list" "list"

Cluster markers config

## $CLUSTER_MARKERS_SOURCES_DEFAULTS
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$COMMON_PARAMS
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$COMMON_PARAMS$PLOT_DIMREDS
## [1] "umap"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$COMMON_PARAMS$BLOCK_COLUMN
## NULL
## 
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$LFC_DIRECTION
## [1] "up"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$LFC_TEST
## [1] 0
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$PVAL_TYPE
## [1] "any"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$MIN_PROP
## NULL
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$STD_LFC
## [1] FALSE
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$TOP_N_HEATMAP
## [1] 3
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$TOP_N_WT_HEATMAP
## [1] "top"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$TOP_N_PLOT
## [1] 3
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_T$TOP_N_WT_PLOT
## [1] "top"
## 
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$LFC_DIRECTION
## [1] "up"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$LFC_TEST
## [1] 0
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$PVAL_TYPE
## [1] "any"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$MIN_PROP
## NULL
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$STD_LFC
## NULL
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$TOP_N_HEATMAP
## [1] 3
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$TOP_N_WT_HEATMAP
## [1] "top"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$TOP_N_PLOT
## [1] 3
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_WILCOX$TOP_N_WT_PLOT
## [1] "top"
## 
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$LFC_DIRECTION
## [1] "up"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$LFC_TEST
## [1] 0
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$PVAL_TYPE
## [1] "any"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$MIN_PROP
## NULL
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$STD_LFC
## NULL
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$TOP_N_HEATMAP
## [1] 3
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$TOP_N_WT_HEATMAP
## [1] "top"
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$TOP_N_PLOT
## [1] 3
## 
## $CLUSTER_MARKERS_SOURCES_DEFAULTS$PARAMS_BINOM$TOP_N_WT_PLOT
## [1] "top"
## 
## 
## 
## $CLUSTER_MARKERS_SOURCES
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$source_column
## [1] "cluster_graph_louvain_r0.4"
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$description
## [1] "Cluster markers for Louvain clustering (r = 0.4)"
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$common_params
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$common_params$plot_dimreds
## [1] "umap" "pca" 
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$common_params$block_column
## NULL
## 
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$params_t
## $lfc_direction
## [1] "up"
## 
## $lfc_test
## [1] 0
## 
## $pval_type
## [1] "some"
## 
## $min_prop
## NULL
## 
## $std_lfc
## [1] FALSE
## 
## $top_n_heatmap
## [1] 3
## 
## $top_n_wt_heatmap
## [1] "fdr"
## 
## $top_n_plot
## [1] 3
## 
## $top_n_wt_plot
## [1] "fdr"
## 
## $test_label
## [1] "t-test"
## 
## $test_dirname
## [1] "t_test"
## 
## attr(,"class")
## [1] "scdrake_list" "list"        
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$name
## [1] "markers_cluster_graph_louvain_r0.4"
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$params_wilcox
## $lfc_direction
## [1] "up"
## 
## $lfc_test
## [1] 0
## 
## $pval_type
## [1] "any"
## 
## $min_prop
## NULL
## 
## $std_lfc
## NULL
## 
## $top_n_heatmap
## [1] 3
## 
## $top_n_wt_heatmap
## [1] "top"
## 
## $top_n_plot
## [1] 3
## 
## $top_n_wt_plot
## [1] "top"
## 
## $test_label
## [1] "Wilcox test"
## 
## $test_dirname
## [1] "wilcox_test"
## 
## attr(,"class")
## [1] "scdrake_list" "list"        
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.4$params_binom
## $lfc_direction
## [1] "up"
## 
## $lfc_test
## [1] 0
## 
## $pval_type
## [1] "any"
## 
## $min_prop
## NULL
## 
## $std_lfc
## NULL
## 
## $top_n_heatmap
## [1] 3
## 
## $top_n_wt_heatmap
## [1] "top"
## 
## $top_n_plot
## [1] 3
## 
## $top_n_wt_plot
## [1] "top"
## 
## $test_label
## [1] "Binomial test"
## 
## $test_dirname
## [1] "binomial_test"
## 
## attr(,"class")
## [1] "scdrake_list" "list"        
## 
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$source_column
## [1] "cluster_graph_louvain_r0.8"
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$description
## [1] "Cluster markers for Louvain clustering (r = 0.8) with blocking on cell cycle phase"
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$common_params
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$common_params$plot_dimreds
## [1] "umap"
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$common_params$block_column
## [1] "phase"
## 
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$name
## [1] "markers_cluster_graph_louvain_r0.8_phase_block"
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$params_t
## $lfc_direction
## [1] "up"
## 
## $lfc_test
## [1] 0
## 
## $pval_type
## [1] "any"
## 
## $min_prop
## NULL
## 
## $std_lfc
## [1] FALSE
## 
## $top_n_heatmap
## [1] 3
## 
## $top_n_wt_heatmap
## [1] "top"
## 
## $top_n_plot
## [1] 3
## 
## $top_n_wt_plot
## [1] "top"
## 
## $test_label
## [1] "t-test"
## 
## $test_dirname
## [1] "t_test"
## 
## attr(,"class")
## [1] "scdrake_list" "list"        
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$params_wilcox
## $lfc_direction
## [1] "up"
## 
## $lfc_test
## [1] 0
## 
## $pval_type
## [1] "any"
## 
## $min_prop
## NULL
## 
## $std_lfc
## NULL
## 
## $top_n_heatmap
## [1] 3
## 
## $top_n_wt_heatmap
## [1] "top"
## 
## $top_n_plot
## [1] 3
## 
## $top_n_wt_plot
## [1] "top"
## 
## $test_label
## [1] "Wilcox test"
## 
## $test_dirname
## [1] "wilcox_test"
## 
## attr(,"class")
## [1] "scdrake_list" "list"        
## 
## $CLUSTER_MARKERS_SOURCES$markers_cluster_graph_louvain_r0.8_phase_block$params_binom
## $lfc_direction
## [1] "up"
## 
## $lfc_test
## [1] 0
## 
## $pval_type
## [1] "any"
## 
## $min_prop
## NULL
## 
## $std_lfc
## NULL
## 
## $top_n_heatmap
## [1] 3
## 
## $top_n_wt_heatmap
## [1] "top"
## 
## $top_n_plot
## [1] 3
## 
## $top_n_wt_plot
## [1] "top"
## 
## $test_label
## [1] "Binomial test"
## 
## $test_dirname
## [1] "binomial_test"
## 
## attr(,"class")
## [1] "scdrake_list" "list"        
## 
## 
## 
## $MAKE_CLUSTER_MARKERS_PLOTS
## [1] TRUE
## 
## $CLUSTER_MARKERS_TABLE_TEMPLATE_RMD_FILE
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/Rmd/common/cluster_markers_table_template.Rmd"
## 
## $CLUSTER_MARKERS_REPORT_RMD_FILE
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/Rmd/common/cluster_markers.Rmd"
## 
## $CLUSTER_MARKERS_BASE_OUT_DIR
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/output/cluster_markers"
## 
## $CLUSTER_MARKERS_REPORT_HTML_FILE
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/output/cluster_markers/cluster_markers.html"
## 
## $CLUSTER_MARKERS_HEATMAPS_OUT_DIR
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/output/cluster_markers/cluster_markers_heatmaps"
## 
## $CLUSTER_MARKERS_PLOTS_BASE_OUT_DIR
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/output/cluster_markers/cluster_markers_plots"
## 
## $CLUSTER_MARKERS_DIMRED_PLOTS_BASE_OUT_DIR
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/output/cluster_markers/cluster_markers_dimred_plots"
## 
## $CLUSTER_MARKERS_TABLES_OUT_DIR
## [1] "/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/output/cluster_markers/cluster_markers_tables"
## 
## attr(,"class")
## [1] "scdrake_list" "list"

Show runtime info

drake cache directory

/home/rstudio/shared/scdrake_run_tests_20231202_01-1.5.1-bioc3.15-docker/pipeline_outputs/example_data/pbmc1k/.drake

Traceback and warnings

## No traceback available

Bioconductor version

3.15

External libs

##                                                      zlib 
##                                                  "1.2.11" 
##                                                     bzlib 
##                                      "1.0.8, 13-Jul-2019" 
##                                                        xz 
##                                                   "5.2.4" 
##                                                      PCRE 
##                                        "10.34 2019-11-21" 
##                                                       ICU 
##                                                    "66.1" 
##                                                       TRE 
##                                 "TRE 0.8.0 R_fixes (BSD)" 
##                                                     iconv 
##                                              "glibc 2.31" 
##                                                  readline 
##                                                     "8.0" 
##                                                      BLAS 
## "/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3"

Session info (pretty)

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.2.1 (2022-06-23)
##  os       Ubuntu 20.04.4 LTS
##  system   x86_64, linux-gnu
##  ui       X11
##  language en
##  collate  C
##  ctype    en_US.UTF-8
##  tz       Etc/UTC
##  date     2023-12-02
##  pandoc   2.18 @ /usr/local/bin/ (via rmarkdown)
## 
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##     GenomicAlignments        1.32.1     2022-07-24 [1] Bioconductor
##     GenomicFeatures        * 1.48.4     2022-09-20 [1] Bioconductor
##     GenomicRanges          * 1.48.0     2022-04-26 [1] Bioconductor
##     ggbeeswarm               0.6.0      2017-08-07 [1] RSPM (R 4.2.0)
##     ggforce                  0.4.1      2022-10-04 [1] RSPM (R 4.2.0)
##     ggplot2                  3.4.0      2022-11-04 [1] RSPM (R 4.2.0)
##     ggplotify                0.1.0      2021-09-02 [1] RSPM (R 4.2.0)
##     ggraph                   2.1.0      2022-10-09 [1] RSPM (R 4.2.0)
##     ggrepel                  0.9.2      2022-11-06 [1] RSPM (R 4.2.0)
##     ggridges                 0.5.4      2022-09-26 [1] RSPM (R 4.2.0)
##     glmGamPoi                1.8.0      2022-04-26 [1] Bioconductor
##     globals                  0.16.2     2022-11-21 [1] RSPM (R 4.2.0)
##     glue                     1.6.2      2022-02-24 [1] CRAN (R 4.2.0)
##     goftest                  1.2-3      2021-10-07 [1] RSPM (R 4.2.0)
##     graphlayouts             0.8.4      2022-11-24 [1] RSPM (R 4.2.0)
##     gridExtra                2.3        2017-09-09 [1] CRAN (R 4.2.0)
##     gridGraphics             0.5-1      2020-12-13 [1] RSPM (R 4.2.0)
##     gtable                   0.3.1      2022-09-01 [1] RSPM (R 4.2.0)
##     harmony                  0.1.1      2022-11-14 [1] RSPM (R 4.2.0)
##     HDF5Array              * 1.24.2     2022-08-02 [1] Bioconductor
##     here                   * 1.0.1      2020-12-13 [1] RSPM (R 4.2.0)
##     highr                    0.9        2021-04-16 [1] CRAN (R 4.2.0)
##     hms                      1.1.2      2022-08-19 [1] RSPM (R 4.2.0)
##     htmltools                0.5.3      2022-07-18 [1] RSPM (R 4.2.0)
##     htmlwidgets              1.5.4      2021-09-08 [1] CRAN (R 4.2.0)
##     httpuv                   1.6.6      2022-09-08 [1] RSPM (R 4.2.0)
##     httr                     1.4.4      2022-08-17 [1] RSPM (R 4.2.0)
##     ica                      1.0-3      2022-07-08 [1] RSPM (R 4.2.0)
##     igraph                   1.3.5      2022-09-22 [1] RSPM (R 4.2.0)
##     interactiveDisplayBase   1.34.0     2022-04-26 [1] Bioconductor
##     IRanges                * 2.30.1     2022-08-18 [1] Bioconductor
##     irlba                    2.3.5.1    2022-10-03 [1] RSPM (R 4.2.0)
##     janitor                  2.1.0      2021-01-05 [1] RSPM (R 4.2.0)
##     jquerylib                0.1.4      2021-04-26 [1] CRAN (R 4.2.0)
##     jsonlite                 1.8.4      2022-12-06 [1] RSPM (R 4.2.0)
##     kableExtra               1.3.4      2021-02-20 [1] RSPM (R 4.2.0)
##     KEGGREST                 1.36.3     2022-07-12 [1] Bioconductor
##     KernSmooth               2.23-20    2021-05-03 [2] CRAN (R 4.2.1)
##     knitr                    1.41       2022-11-18 [1] RSPM (R 4.2.0)
##     labeling                 0.4.2      2020-10-20 [1] CRAN (R 4.2.0)
##     later                    1.3.0      2021-08-18 [1] CRAN (R 4.2.0)
##     lattice                  0.20-45    2021-09-22 [2] CRAN (R 4.2.1)
##     lazyeval                 0.2.2      2019-03-15 [1] CRAN (R 4.2.0)
##     leiden                   0.4.3      2022-09-10 [1] RSPM (R 4.2.0)
##     lifecycle                1.0.3      2022-10-07 [1] RSPM (R 4.2.0)
##     limma                    3.52.4     2022-09-27 [1] Bioconductor
##     listenv                  0.8.0      2019-12-05 [1] RSPM (R 4.2.0)
##     littler                  0.3.17     2023-05-26 [1] Github (eddelbuettel/littler@31aa160)
##     lmtest                   0.9-40     2022-03-21 [1] RSPM (R 4.2.0)
##     locfit                   1.5-9.6    2022-07-11 [1] RSPM (R 4.2.0)
##     lubridate                1.9.0      2022-11-06 [1] RSPM (R 4.2.0)
##     magrittr               * 2.0.3      2022-03-30 [1] CRAN (R 4.2.0)
##     MASS                     7.3-58.1   2022-08-03 [2] RSPM (R 4.2.0)
##     Matrix                 * 1.5-3      2022-11-11 [1] RSPM (R 4.2.0)
##     MatrixGenerics         * 1.8.1      2022-06-26 [1] Bioconductor
##     matrixStats            * 0.63.0     2022-11-18 [1] RSPM (R 4.2.0)
##     memoise                  2.0.1      2021-11-26 [1] CRAN (R 4.2.0)
##     metapod                  1.4.0      2022-04-26 [1] Bioconductor
##     mime                     0.12       2021-09-28 [1] CRAN (R 4.2.0)
##     miniUI                   0.1.1.1    2018-05-18 [1] RSPM (R 4.2.0)
##     munsell                  0.5.0      2018-06-12 [1] CRAN (R 4.2.0)
##     mvtnorm                  1.1-3      2021-10-08 [1] CRAN (R 4.2.0)
##     nlme                     3.1-158    2022-06-15 [2] RSPM (R 4.2.0)
##     org.Hs.eg.db             3.15.0     2022-04-11 [1] Bioconductor
##     parallelly               1.32.1     2022-07-21 [1] RSPM (R 4.2.0)
##     patchwork                1.1.2      2022-08-19 [1] RSPM (R 4.2.0)
##     pbapply                  1.6-0      2022-11-16 [1] RSPM (R 4.2.0)
##     pcaPP                    2.0-3      2022-10-24 [1] RSPM (R 4.2.0)
##     PCAtools                 2.8.0      2022-04-26 [1] Bioconductor
##     pheatmap                 1.0.12     2019-01-04 [1] RSPM (R 4.2.0)
##     pillar                   1.8.1      2022-08-19 [1] RSPM (R 4.2.0)
##     pkgbuild                 1.3.1      2021-12-20 [1] RSPM (R 4.2.0)
##     pkgconfig                2.0.3      2019-09-22 [1] CRAN (R 4.2.0)
##     pkgload                  1.3.2      2022-11-16 [1] RSPM (R 4.2.0)
##     plotly                   4.10.1     2022-11-07 [1] RSPM (R 4.2.0)
##     plyr                     1.8.8      2022-11-11 [1] RSPM (R 4.2.0)
##     png                      0.1-8      2022-11-29 [1] RSPM (R 4.2.0)
##     polyclip                 1.10-4     2022-10-20 [1] RSPM (R 4.2.0)
##     prettyunits              1.1.1      2020-01-24 [1] CRAN (R 4.2.0)
##     processx                 3.8.0      2022-10-26 [1] RSPM (R 4.2.0)
##     profvis                  0.3.7      2020-11-02 [1] RSPM (R 4.2.0)
##     progress                 1.2.2      2019-05-16 [1] CRAN (R 4.2.0)
##     progressr                0.11.0     2022-09-02 [1] RSPM (R 4.2.0)
##     promises                 1.2.0.1    2021-02-11 [1] CRAN (R 4.2.0)
##     ProtGenerics             1.28.0     2022-04-26 [1] Bioconductor
##     proxy                    0.4-27     2022-06-09 [1] RSPM (R 4.2.0)
##     ps                       1.7.2      2022-10-26 [1] RSPM (R 4.2.0)
##     purrr                    0.3.5      2022-10-06 [1] RSPM (R 4.2.0)
##     qs                       0.25.4     2022-08-09 [1] RSPM (R 4.2.0)
##     R.methodsS3              1.8.2      2022-06-13 [1] RSPM (R 4.2.0)
##     R.oo                     1.25.0     2022-06-12 [1] RSPM (R 4.2.0)
##     R.utils                  2.12.2     2022-11-11 [1] RSPM (R 4.2.0)
##     R6                       2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
##     ragg                     1.2.4      2022-10-24 [1] RSPM (R 4.2.0)
##     RANN                     2.6.1      2019-01-08 [1] RSPM (R 4.2.0)
##     RApiSerialize            0.1.2      2022-08-25 [1] RSPM (R 4.2.0)
##     rappdirs                 0.3.3      2021-01-31 [1] CRAN (R 4.2.0)
##     RColorBrewer             1.1-3      2022-04-03 [1] CRAN (R 4.2.0)
##     Rcpp                     1.0.9      2022-07-08 [1] RSPM (R 4.2.0)
##     RcppAnnoy                0.0.20     2022-10-27 [1] RSPM (R 4.2.0)
##     RcppParallel             5.1.5      2022-01-05 [1] RSPM (R 4.2.0)
##     RCurl                    1.98-1.9   2022-10-03 [1] RSPM (R 4.2.0)
##     readr                    2.1.3      2022-10-01 [1] RSPM (R 4.2.0)
##     remotes                  2.4.2      2021-11-30 [1] RSPM (R 4.2.0)
##     reshape2                 1.4.4      2020-04-09 [1] CRAN (R 4.2.0)
##     ResidualMatrix           1.6.1      2022-08-16 [1] Bioconductor
##     restfulr                 0.0.15     2022-06-16 [1] RSPM (R 4.2.0)
##     reticulate               1.26       2022-08-31 [1] RSPM (R 4.2.0)
##     rhdf5                  * 2.40.0     2022-04-26 [1] Bioconductor
##     rhdf5filters             1.8.0      2022-04-26 [1] Bioconductor
##     Rhdf5lib                 1.18.2     2022-05-15 [1] Bioconductor
##     RhpcBLASctl              0.21-247.1 2021-11-05 [1] RSPM (R 4.2.0)
##     rjson                    0.2.21     2022-01-09 [1] CRAN (R 4.2.0)
##     rlang                  * 1.0.6      2022-09-24 [1] RSPM (R 4.2.0)
##     rmarkdown                2.18       2022-11-09 [1] RSPM (R 4.2.0)
##     robustbase               0.95-0     2022-04-02 [1] CRAN (R 4.2.0)
##     ROCR                     1.0-11     2020-05-02 [1] CRAN (R 4.2.0)
##     rprojroot                2.0.3      2022-04-02 [1] CRAN (R 4.2.0)
##     rrcov                    1.7-2      2022-10-24 [1] RSPM (R 4.2.0)
##     Rsamtools                2.12.0     2022-04-26 [1] Bioconductor
##     RSQLite                  2.2.19     2022-11-24 [1] RSPM (R 4.2.0)
##     rstudioapi               0.14       2022-08-22 [1] RSPM (R 4.2.0)
##     rsvd                     1.0.5      2021-04-16 [1] RSPM (R 4.2.0)
##     rtracklayer              1.56.1     2022-06-23 [1] Bioconductor
##     Rtsne                    0.16       2022-04-17 [1] RSPM (R 4.2.0)
##     rvest                    1.0.3      2022-08-19 [1] RSPM (R 4.2.0)
##     rzmq                     0.9.8      2021-05-04 [1] RSPM (R 4.2.0)
##     S4Vectors              * 0.34.0     2022-04-26 [1] Bioconductor
##     sass                     0.4.4      2022-11-24 [1] RSPM (R 4.2.0)
##     SC3                      1.15.1     2023-05-26 [1] Github (gorgitko/SC3@58d73fb)
##     ScaledMatrix             1.4.1      2022-09-11 [1] Bioconductor
##     scales                   1.2.1      2022-08-20 [1] RSPM (R 4.2.0)
##     scater                   1.24.0     2022-04-26 [1] Bioconductor
##     scattermore              0.8        2022-02-14 [1] RSPM (R 4.2.0)
##     scDblFinder              1.10.0     2022-04-26 [1] Bioconductor
##  VP scdrake                * 1.5.1      2023-06-15 [?] Bioconductor (on disk 1.5.0)
##     scran                    1.24.1     2022-09-11 [1] Bioconductor
##     sctransform              0.3.5      2022-09-21 [1] RSPM (R 4.2.0)
##     scuttle                  1.6.3      2022-08-23 [1] Bioconductor
##     sessioninfo              1.2.2      2021-12-06 [1] RSPM (R 4.2.0)
##     Seurat                   4.3.0      2022-11-18 [1] RSPM (R 4.2.0)
##     SeuratObject             4.1.3      2022-11-07 [1] RSPM (R 4.2.0)
##     shiny                    1.7.3      2022-10-25 [1] RSPM (R 4.2.0)
##     SingleCellExperiment     1.18.1     2022-10-02 [1] Bioconductor
##     SingleR                  1.10.0     2022-04-26 [1] Bioconductor
##     snakecase                0.11.0     2019-05-25 [1] RSPM (R 4.2.0)
##     sp                       1.5-1      2022-11-07 [1] RSPM (R 4.2.0)
##     sparseMatrixStats        1.8.0      2022-04-26 [1] Bioconductor
##     spatstat.data            3.0-0      2022-10-21 [1] RSPM (R 4.2.0)
##     spatstat.explore         3.0-5      2022-11-10 [1] RSPM (R 4.2.0)
##     spatstat.geom            3.0-3      2022-10-25 [1] RSPM (R 4.2.0)
##     spatstat.random          3.0-1      2022-11-03 [1] RSPM (R 4.2.0)
##     spatstat.sparse          3.0-0      2022-10-21 [1] RSPM (R 4.2.0)
##     spatstat.utils           3.0-1      2022-10-19 [1] RSPM (R 4.2.0)
##     statmod                  1.4.37     2022-08-12 [1] RSPM (R 4.2.0)
##     storr                    1.2.5      2020-12-01 [1] RSPM (R 4.2.0)
##     stringfish               0.15.7     2022-04-13 [1] RSPM (R 4.2.0)
##     stringi                  1.7.8      2022-07-11 [1] RSPM (R 4.2.0)
##     stringr                  1.5.0      2022-12-02 [1] RSPM (R 4.2.0)
##     SummarizedExperiment     1.26.1     2022-04-29 [1] Bioconductor
##     survival                 3.3-1      2022-03-03 [2] CRAN (R 4.2.1)
##     svglite                  2.1.0      2022-02-03 [1] RSPM (R 4.2.0)
##     systemfonts              1.0.4      2022-02-11 [1] RSPM (R 4.2.0)
##     tensor                   1.5        2012-05-05 [1] RSPM (R 4.2.0)
##     testthat               * 3.1.5      2022-10-08 [1] RSPM (R 4.2.0)
##     textshaping              0.3.6      2021-10-13 [1] RSPM (R 4.2.0)
##     tibble                   3.1.8      2022-07-22 [1] RSPM (R 4.2.0)
##     tidygraph                1.2.3      2023-02-01 [1] RSPM (R 4.2.0)
##     tidyr                    1.2.1      2022-09-08 [1] RSPM (R 4.2.0)
##     tidyselect               1.1.2      2022-02-21 [1] RSPM (R 4.2.0)
##     timechange               0.1.1      2022-11-04 [1] RSPM (R 4.2.0)
##     tweenr                   2.0.2      2022-09-06 [1] RSPM (R 4.2.0)
##     txtq                     0.2.4      2021-03-27 [1] RSPM (R 4.2.0)
##     tzdb                     0.3.0      2022-03-28 [1] CRAN (R 4.2.0)
##     urlchecker               1.0.1      2021-11-30 [1] RSPM (R 4.2.0)
##     usethis                  2.1.6      2022-05-25 [1] RSPM (R 4.2.0)
##     utf8                     1.2.2      2021-07-24 [1] CRAN (R 4.2.0)
##     uwot                     0.1.14     2022-08-22 [1] RSPM (R 4.2.0)
##     vctrs                    0.5.1      2022-11-16 [1] RSPM (R 4.2.0)
##     vipor                    0.4.5      2017-03-22 [1] RSPM (R 4.2.0)
##     viridis                  0.6.2      2021-10-13 [1] CRAN (R 4.2.0)
##     viridisLite              0.4.1      2022-08-22 [1] RSPM (R 4.2.0)
##     webshot                  0.5.4      2022-09-26 [1] RSPM (R 4.2.0)
##     withr                    2.5.0      2022-03-03 [1] CRAN (R 4.2.0)
##     WriteXLS                 6.4.0      2022-02-24 [1] RSPM (R 4.2.0)
##     xfun                     0.35       2022-11-16 [1] RSPM (R 4.2.0)
##     xgboost                  1.6.0.1    2022-04-16 [1] RSPM (R 4.2.0)
##     XML                      3.99-0.13  2022-12-04 [1] RSPM (R 4.2.0)
##     xml2                     1.3.3      2021-11-30 [1] CRAN (R 4.2.0)
##     xtable                   1.8-4      2019-04-21 [1] CRAN (R 4.2.0)
##     XVector                  0.36.0     2022-04-26 [1] Bioconductor
##     yaml                     2.3.6      2022-10-18 [1] RSPM (R 4.2.0)
##     yulab.utils              0.0.5      2022-06-30 [1] RSPM (R 4.2.0)
##     zlibbioc                 1.42.0     2022-04-26 [1] Bioconductor
##     zoo                      1.8-11     2022-09-17 [1] RSPM (R 4.2.0)
## 
##  [1] /usr/local/lib/R/site-library
##  [2] /usr/local/lib/R/library
## 
##  V ── Loaded and on-disk version mismatch.
##  P ── Loaded and on-disk path mismatch.
## 
## ──────────────────────────────────────────────────────────────────────────────

Session info (base)

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats    graphics stats4   utils    methods  base    
## 
## other attached packages:
##  [1] ensembldb_2.20.2        AnnotationFilter_1.20.0 GenomicFeatures_1.48.4 
##  [4] GenomicRanges_1.48.0    GenomeInfoDb_1.32.4     HDF5Array_1.24.2       
##  [7] rhdf5_2.40.0            DelayedArray_0.22.0     MatrixGenerics_1.8.1   
## [10] matrixStats_0.63.0      Matrix_1.5-3            drake_7.13.4           
## [13] AnnotationDbi_1.58.0    IRanges_2.30.1          S4Vectors_0.34.0       
## [16] Biobase_2.56.0          BiocGenerics_0.42.0     scdrake_1.5.1          
## [19] testthat_3.1.5          magrittr_2.0.3          here_1.0.1             
## [22] cli_3.4.1               rlang_1.0.6             conflicted_1.1.0       
## 
## loaded via a namespace (and not attached):
##   [1] rsvd_1.0.5                    ica_1.0-3                    
##   [3] svglite_2.1.0                 class_7.3-20                 
##   [5] ps_1.7.2                      Rsamtools_2.12.0             
##   [7] lmtest_0.9-40                 rprojroot_2.0.3              
##   [9] crayon_1.5.2                  MASS_7.3-58.1                
##  [11] rhdf5filters_1.8.0            nlme_3.1-158                 
##  [13] WriteXLS_6.4.0                backports_1.4.1              
##  [15] XVector_0.36.0                ROCR_1.0-11                  
##  [17] irlba_2.3.5.1                 callr_3.7.3                  
##  [19] limma_3.52.4                  scater_1.24.0                
##  [21] filelock_1.0.2                stringfish_0.15.7            
##  [23] xgboost_1.6.0.1               qs_0.25.4                    
##  [25] BiocParallel_1.30.4           rjson_0.2.21                 
##  [27] bit64_4.0.5                   glue_1.6.2                   
##  [29] harmony_0.1.1                 scDblFinder_1.10.0           
##  [31] pheatmap_1.0.12               sctransform_0.3.5            
##  [33] parallel_4.2.1                processx_3.8.0               
##  [35] vipor_0.4.5                   spatstat.sparse_3.0-0        
##  [37] base64url_1.4                 spatstat.geom_3.0-3          
##  [39] tidyselect_1.1.2              SummarizedExperiment_1.26.1  
##  [41] usethis_2.1.6                 argparser_0.7.1              
##  [43] SeuratObject_4.1.3            fitdistrplus_1.1-8           
##  [45] XML_3.99-0.13                 tidyr_1.2.1                  
##  [47] zoo_1.8-11                    GenomicAlignments_1.32.1     
##  [49] xtable_1.8-4                  evaluate_0.18                
##  [51] ggplot2_3.4.0                 scuttle_1.6.3                
##  [53] zlibbioc_1.42.0               rstudioapi_0.14              
##  [55] miniUI_0.1.1.1                sp_1.5-1                     
##  [57] bslib_0.4.1                   shiny_1.7.3                  
##  [59] BiocSingular_1.12.0           xfun_0.35                    
##  [61] pkgbuild_1.3.1                cluster_2.1.3                
##  [63] tidygraph_1.2.3               KEGGREST_1.36.3              
##  [65] clustermq_0.8.8               tibble_3.1.8                 
##  [67] interactiveDisplayBase_1.34.0 ggrepel_0.9.2                
##  [69] listenv_0.8.0                 Biostrings_2.64.1            
##  [71] png_0.1-8                     future_1.29.0                
##  [73] withr_2.5.0                   bitops_1.0-7                 
##  [75] ggforce_0.4.1                 plyr_1.8.8                   
##  [77] pcaPP_2.0-3                   e1071_1.7-12                 
##  [79] dqrng_0.3.0                   RcppParallel_5.1.5           
##  [81] pillar_1.8.1                  cachem_1.0.6                 
##  [83] fs_1.5.2                      DelayedMatrixStats_1.18.2    
##  [85] vctrs_0.5.1                   ellipsis_0.3.2               
##  [87] generics_0.1.3                RApiSerialize_0.1.2          
##  [89] devtools_2.4.4                tools_4.2.1                  
##  [91] beeswarm_0.4.0                munsell_0.5.0                
##  [93] tweenr_2.0.2                  proxy_0.4-27                 
##  [95] fastmap_1.1.0                 compiler_4.2.1               
##  [97] pkgload_1.3.2                 abind_1.4-5                  
##  [99] httpuv_1.6.6                  rtracklayer_1.56.1           
## [101] ExperimentHub_2.4.0           sessioninfo_1.2.2            
## [103] plotly_4.10.1                 GenomeInfoDbData_1.2.8       
## [105] gridExtra_2.3                 edgeR_3.38.4                 
## [107] lattice_0.20-45               deldir_1.0-6                 
## [109] utf8_1.2.2                    later_1.3.0                  
## [111] dplyr_1.0.10                  BiocFileCache_2.4.0          
## [113] jsonlite_1.8.4                storr_1.2.5                  
## [115] scales_1.2.1                  datasets_4.2.1               
## [117] ScaledMatrix_1.4.1            pbapply_1.6-0                
## [119] sparseMatrixStats_1.8.0       lazyeval_0.2.2               
## [121] promises_1.2.0.1              R.utils_2.12.2               
## [123] goftest_1.2-3                 spatstat.utils_3.0-1         
## [125] reticulate_1.26               rmarkdown_2.18               
## [127] cowplot_1.1.1                 textshaping_0.3.6            
## [129] statmod_1.4.37                webshot_0.5.4                
## [131] Rtsne_0.16                    glmGamPoi_1.8.0              
## [133] uwot_0.1.14                   igraph_1.3.5                 
## [135] survival_3.3-1                ResidualMatrix_1.6.1         
## [137] yaml_2.3.6                    systemfonts_1.0.4            
## [139] htmltools_0.5.3               memoise_2.0.1                
## [141] profvis_0.3.7                 BiocIO_1.6.0                 
## [143] Seurat_4.3.0                  locfit_1.5-9.6               
## [145] graphlayouts_0.8.4            PCAtools_2.8.0               
## [147] viridisLite_0.4.1             digest_0.6.30                
## [149] rrcov_1.7-2                   assertthat_0.2.1             
## [151] RhpcBLASctl_0.21-247.1        mime_0.12                    
## [153] rappdirs_0.3.3                SingleR_1.10.0               
## [155] RSQLite_2.2.19                yulab.utils_0.0.5            
## [157] future.apply_1.10.0           remotes_2.4.2                
## [159] data.table_1.14.6             urlchecker_1.0.1             
## [161] blob_1.2.3                    R.oo_1.25.0                  
## [163] ragg_1.2.4                    labeling_0.4.2               
## [165] splines_4.2.1                 Rhdf5lib_1.18.2              
## [167] AnnotationHub_3.4.0           ProtGenerics_1.28.0          
## [169] RCurl_1.98-1.9                hms_1.1.2                    
## [171] colorspace_2.0-3              DropletUtils_1.16.0          
## [173] BiocManager_1.30.19           ggbeeswarm_0.6.0             
## [175] littler_0.3.17                sass_0.4.4                   
## [177] Rcpp_1.0.9                    RANN_2.6.1                   
## [179] mvtnorm_1.1-3                 txtq_0.2.4                   
## [181] fansi_1.0.3                   tzdb_0.3.0                   
## [183] brio_1.1.3                    parallelly_1.32.1            
## [185] R6_2.5.1                      grid_4.2.1                   
## [187] ggridges_0.5.4                lifecycle_1.0.3              
## [189] bluster_1.6.0                 curl_4.3.3                   
## [191] jquerylib_0.1.4               leiden_0.4.3                 
## [193] snakecase_0.11.0              robustbase_0.95-0            
## [195] desc_1.4.2                    RcppAnnoy_0.0.20             
## [197] org.Hs.eg.db_3.15.0           RColorBrewer_1.1-3           
## [199] spatstat.explore_3.0-5        stringr_1.5.0                
## [201] htmlwidgets_1.5.4             beachmat_2.12.0              
## [203] polyclip_1.10-4               biomaRt_2.52.0               
## [205] purrr_0.3.5                   crosstalk_1.2.0              
## [207] timechange_0.1.1              gridGraphics_0.5-1           
## [209] rvest_1.0.3                   globals_0.16.2               
## [211] spatstat.random_3.0-1         patchwork_1.1.2              
## [213] progressr_0.11.0              batchelor_1.12.3             
## [215] codetools_0.2-18              grDevices_4.2.1              
## [217] lubridate_1.9.0               metapod_1.4.0                
## [219] prettyunits_1.1.1             SingleCellExperiment_1.18.1  
## [221] dbplyr_2.2.1                  R.methodsS3_1.8.2            
## [223] celldex_1.6.0                 gtable_0.3.1                 
## [225] DBI_1.1.3                     highr_0.9                    
## [227] tensor_1.5                    httr_1.4.4                   
## [229] KernSmooth_2.23-20            stringi_1.7.8                
## [231] progress_1.2.2                reshape2_1.4.4               
## [233] farver_2.1.1                  viridis_0.6.2                
## [235] DT_0.26                       xml2_1.3.3                   
## [237] BiocNeighbors_1.14.0          kableExtra_1.3.4             
## [239] restfulr_0.0.15               readr_2.1.3                  
## [241] ggplotify_0.1.0               scattermore_0.8              
## [243] BiocVersion_3.15.2            scran_1.24.1                 
## [245] DEoptimR_1.0-11               bit_4.0.5                    
## [247] clustree_0.5.0                spatstat.data_3.0-0          
## [249] ggraph_2.1.0                  janitor_2.1.0                
## [251] pkgconfig_2.0.3               rzmq_0.9.8                   
## [253] knitr_1.41                    downlit_0.4.2                
## [255] SC3_1.15.1

Page generated on 2023-12-02 18:51:26

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