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
- Institute: Example institute
- Laboratory: Example laboratory
- People: Example person 1, Example person 2
1000 peripheral blood mononuclear cells by 10x Genomics
- Organism: human
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 availableBioconductor version
3.15
External libs
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## "1.2.11"
## bzlib
## "1.0.8, 13-Jul-2019"
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## PCRE
## "10.34 2019-11-21"
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## "66.1"
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## "TRE 0.8.0 R_fixes (BSD)"
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## "/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3"Session info (pretty)
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## setting value
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## language en
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## ctype en_US.UTF-8
## tz Etc/UTC
## date 2023-12-02
## pandoc 2.18 @ /usr/local/bin/ (via rmarkdown)
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## 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_1.15.1Page generated on 2023-12-02 18:51:26
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