Last updated: 2021-12-13

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Knit directory: MS_lesions/

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    Modified:   code/supp10_muscat_gsea.R

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File Version Author Date Message
html 7fb1b95 wmacnair 2021-11-25 Host with GitLab.
Rmd 7ddc417 Macnair 2021-09-24 Add pseudobulk version of modules
Rmd 2b5e1cc Macnair 2021-09-03 Tweak ms08_modules
Rmd 1342e46 Macnair 2021-08-24 Update module analysis
Rmd eef8a1c Macnair 2021-04-29 Minor tweaks to allow rerunning on Roche servers
Rmd 129c53d Macnair 2021-04-16 Renamed a lot of things to add ms07_soup

Done

  • redo GSEA with FGSEA
    • add FGSEA calcs to get_pop_results
    • add FGSEA calc to get_pop_results
  • redo GSEA with FGSEA plus randomly ordered other genes

To-do

  • try with pseudobulk instead?

Setup / definitions

Libraries

Helper functions

source('code/ms00_utils.R')
source('code/ms08_modules.R')
source_python('code/ms08_modules.py')

Inputs

# base inputs
sce_f       = 'data/sce_raw/ms_sce.rds'
labels_f    = 'data/byhand_markers/validation_markers_2021-05-31.csv'
labelled_f  = 'output/ms13_labelling/conos_labelled_2021-05-31.txt.gz'
meta_f      = 'data/metadata/metadata_updated_20201127.txt'

# define pseudobulk files
soup_dir    = 'output/ms07_soup'
date_soup   = '2021-06-01'
pb_fine_f   = sprintf('%s/pb_sum_fine_%s.rds', soup_dir, date_soup)
prop_fine_f = sprintf('%s/pb_prop_fine_%s.rds', soup_dir, date_soup)

# broad level pseudobulk files
pb_broad_f  = file.path(soup_dir, 'pb_sum_broad_2021-06-01.rds')
pb_fine_f   = file.path(soup_dir, 'pb_sum_fine_2021-06-01.rds')
prop_fine_f = file.path(soup_dir, 'pb_prop_fine_2021-06-01.rds')
pb_soup_f   = file.path(soup_dir, 'pb_soup_broad_maximum_2021-06-01.rds')
gtf_f       = 'data/gtf/Homo_sapiens.GRCh38.96.filtered.preMRNA.gtf'

Outputs

# set up directory
save_dir    = 'output/ms08_modules'
date_tag    = '2021-08-18'
if (!dir.exists(save_dir))
    dir.create(save_dir)
ncores      = 12

# output file patterns
genes_pat   = sprintf('%s/%s/features_%s_%s.tsv', save_dir, '%s', date_tag, '%s')
mtx_pat     = sprintf('%s/%s/counts_%s_%s.mtx', save_dir, '%s', date_tag, '%s')
sce_pat     = sprintf('%s/%s/sce_sub_%s_%s.rds', save_dir, '%s', date_tag, '%s')
ok_gs_pat   = sprintf('%s/%s/ok_gs_%s_%s.txt', save_dir, '%s', date_tag, '%s')
pop_pat     = sprintf('%s/%s/pop_%s_%s.p', save_dir, '%s', '%s', date_tag)
res_pat     = sprintf('%s/%s/res_%s_%s.rds', save_dir, '%s', date_tag, '%s')
go_pat      = sprintf('%s/%s/go_dt_%s_%s_%s.rds', save_dir, '%s', date_tag, '%s', '%s')

# lists of celltypes for each run
spec_list   = list(
  oligo_opc       = list(type_broad = c('OPCs / COPs', 'Oligodendrocytes')),
  micro_immune    = list(type_broad = c('Microglia', 'Immune')),
  excitatory      = list(type_broad = 'Excitatory neurons'),
  inhibitory      = list(type_broad = 'Inhibitory neurons'),
  astrocytes      = list(type_broad = c('Astrocytes')),
  endo_stromal    = list(type_broad = c('Endothelial cells', 'Pericytes')),
  microglia       = list(type_broad = c('Microglia')),
  immune          = list(type_broad = c('Immune'))
  )
assert_that(length(spec_list) == length(unique(names(spec_list))))
[1] TRUE
group_list  = names(spec_list)

# how many per fine celltype?
n_sample    = 2e3
n_genes     = 2e3
max_soup    = 0.1
ok_types    = 'protein_coding'

# umap params
umap_many_f = 'output/ms04_conos/conos_umap_sub_2021-02-11.txt'
# umap_ps   = list(
#   min_dist    = 0.1,
#   spread      = 8
#   )
umap_ps   = list(
  min_dist    = 1,
  spread      = 2
  )

# define xls file to save
xl_f        = sprintf('%s/modules_genes_%s.xlsx', save_dir, date_tag)
go_xl_f     = sprintf('%s/modules_go_terms_%s.xlsx', save_dir, date_tag)

Load inputs

labels_dt   = load_names_dt(labels_f) %>%
  .[, cluster_id := type_fine]
conos_dt    = load_labelled_dt(labelled_f, labels_f)
meta_dt     = load_meta_dt(meta_f)
pb_soup     = pb_soup_f %>% readRDS
pb_broad    = pb_broad_f %>% readRDS
contam_dt   = calc_contam_dt(pb_soup, pb_broad, min_cells = 10)
rm(pb_soup, pb_broad)
biotypes_dt = get_biotypes_dt(gtf_f)
fine_dt     = load_fine_dt(pb_fine_f, prop_fine_f, labels_dt)
umap_dt     = umap_many_f %>% fread %>% 
  .[ min_dist == umap_ps$min_dist & spread == umap_ps$spread ] %>%
  .[, .(cell_id, UMAP1, UMAP2)]

Processing / calculations

save_sub_sces(spec_list, sce_f, sce_pat, ok_gs_pat, conos_dt, contam_dt, 
  biotypes_dt, n_sample, n_genes, max_soup, ok_types, save_dir)
already done!
NULL
save_outputs_for_popalign(group_list, sce_pat, mtx_pat, genes_pat)
already done!
NULL
run_onmf(save_dir, date_tag, group_list, ncores = ncores)
pop_list    = group_list %>%
  map(~get_pop_results(.x, res_pat, sce_pat, ok_gs_pat, go_pat, pop_pat, 
    conos_dt)) %>% setNames(group_list)

Analysis

Median module scores by celltype (scaled)

for (g in group_list) {
  cat('### ', g, '\n')
  hm = plot_scores_by_celltype(pop_list[[g]]$scores_dt, pop_list[[g]]$k_order,
    what = 'scaled')
  if (!is.null(hm))
    draw(hm)
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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Median module scores by celltype (proportions)

for (g in group_list) {
  cat('### ', g, '\n')
  hm = plot_scores_by_celltype(pop_list[[g]]$scores_dt, pop_list[[g]]$k_order,
    what = 'propns')
  if (!is.null(hm))
    draw(hm)
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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Distribution of module scores over UMAP

for (g in group_list) {
  cat('### ', g, '\n')
  print(plot_scores_over_umap(pop_list[[g]]$scores_dt, pop_list[[g]]$k_order, umap_dt))
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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Most important genes per module

for (g in group_list) {
  cat('### ', g, '\n')
  print(plot_biggest_genes_dotplot(g, spec_list, pop_list[[g]]$w_mat, 
    pop_list[[g]]$k_order, fine_dt, w2_cut = 0.02))
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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for (g in group_list) {
  cat('### ', g, '\n')
  hm  = plot_biggest_genes(pop_list[[g]]$w_mat, pop_list[[g]]$k_order, 
    w2_cut = 0.02)
  if (!is.null(hm))
    draw(hm)
  cat('\n\n')
}

Distribution of top genes over UMAP

for (g in group_list) {
  cat('### ', g, '\n')
  print(plot_genes_over_umap(pop_list[[g]]$genes_dt, umap_dt))
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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Median module scores by celltype (scaled)

for (g in group_list) {
  cat('### ', g, '\n')
  hm = plot_scores_by_celltype(pop_list[[g]]$scores_dt, pop_list[[g]]$k_order,
    what = 'scaled')
  if (!is.null(hm))
    draw(hm)
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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Enriched GO terms per module (using 2k genes for GSEA)

source('code/ms08_modules.R')
for (g in group_list) {
  cat('### ', g, '\n')
  hm  = plot_enriched_sets(pop_list[[g]]$go_std_dt, pop_list[[g]]$k_order)
  if (!is.null(hm))
    draw(hm)
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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Enriched GO terms per module (using more genes for GSEA)

for (g in group_list) {
  cat('### ', g, '\n')
  hm  = plot_enriched_sets(pop_list[[g]]$go_all_dt, pop_list[[g]]$k_order)
  if (!is.null(hm))
    draw(hm)
  cat('\n\n')
}

oligo_opc

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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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UMAP celltype reference

(plot_umap_celltypes(umap_dt, conos_dt))

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feat_list   = scores_dt$feat %>% unique %>% sort %>% .[k_order]
for (f in feat_list) {
  cat('### ', f, '\n')
  print(plot_scores_over_lesions(scores_dt, f, meta_dt))
  cat('\n\n')
}

Distribution of fine celltypes over UMAP

for (g in group_list) {
  cat('### ', g, '\n')
  print(plot_celltypes_over_umap(spec_list[[g]], conos_dt, umap_dt))
  cat('\n\n')
}

oligo_opc

Version Author Date
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micro_immune

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excitatory

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inhibitory

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astrocytes

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endo_stromal

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microglia

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immune

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Outputs

save_module_genes_to_xl(pop_list, xl_f)
NULL
save_module_go_terms_to_xl(group_list, go_pat, go_xl_f)

Figures

Selected genes over UMAP

g         = 'oligo_opc'
sel_genes = c("TNR", "LRP1B", "CAMK2D", "QKI", "NCAM2", "NLGN1", "KIRREL3", 
  "MBP", "GLUL", "ELL2")
(plot_sel_genes_over_umap(g, pop_list, sce_pat, umap_dt, sel_genes))

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devtools::session_info()
Registered S3 method overwritten by 'cli':
  method     from         
  print.boxx spatstat.geom
- Session info ---------------------------------------------------------------
 setting  value                       
 version  R version 4.0.5 (2021-03-31)
 os       CentOS Linux 7 (Core)       
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    C                           
 tz       Europe/Zurich               
 date     2021-12-13                  

- Packages -------------------------------------------------------------------
 ! package              * version    date       lib
   abind                  1.4-5      2016-07-21 [2]
   annotate               1.68.0     2020-10-27 [1]
   AnnotationDbi          1.52.0     2020-10-27 [1]
   assertthat           * 0.2.1      2019-03-21 [2]
   backports              1.2.1      2020-12-09 [2]
   beachmat               2.6.4      2020-12-20 [1]
   beeswarm               0.4.0      2021-06-01 [1]
   Biobase              * 2.50.0     2020-10-27 [1]
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   BiocNeighbors          1.8.2      2020-12-07 [1]
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   BiocSingular           1.6.0      2020-10-27 [1]
   BiocStyle            * 2.18.1     2020-11-24 [1]
   Biostrings             2.58.0     2020-10-27 [1]
   bit                    4.0.4      2020-08-04 [2]
   bit64                  4.0.5      2020-08-30 [2]
   bitops                 1.0-7      2021-04-24 [2]
   blme                   1.0-5      2021-01-05 [1]
   blob                   1.2.2      2021-07-23 [2]
   boot                   1.3-28     2021-05-03 [2]
   broom                  0.7.9      2021-07-27 [2]
   bslib                  0.3.1      2021-10-06 [2]
   cachem                 1.0.6      2021-08-19 [1]
   Cairo                  1.5-12.2   2020-07-07 [2]
   callr                  3.7.0      2021-04-20 [2]
   caTools                1.18.2     2021-03-28 [2]
   cellranger             1.1.0      2016-07-27 [2]
   circlize             * 0.4.13     2021-06-09 [1]
   cli                    3.0.1      2021-07-17 [1]
   clue                   0.3-60     2021-10-11 [1]
   cluster                2.1.2      2021-04-17 [2]
   codetools              0.2-18     2020-11-04 [2]
   colorout             * 1.2-2      2021-04-15 [1]
   colorRamps             2.3        2012-10-29 [1]
   colorspace             2.0-2      2021-06-24 [1]
   ComplexHeatmap       * 2.6.2      2020-11-12 [1]
   cowplot                1.1.1      2020-12-30 [2]
   crayon                 1.4.1      2021-02-08 [2]
   data.table           * 1.14.2     2021-09-27 [2]
   DBI                    1.1.1      2021-01-15 [2]
   DelayedArray           0.16.3     2021-03-24 [1]
   DelayedMatrixStats     1.12.3     2021-02-03 [1]
   deldir                 1.0-6      2021-10-23 [2]
   desc                   1.4.0      2021-09-28 [1]
   DESeq2                 1.30.1     2021-02-19 [1]
   devtools               2.4.2      2021-06-07 [1]
   digest                 0.6.28     2021-09-23 [2]
   doParallel             1.0.16     2020-10-16 [1]
   dplyr                  1.0.7      2021-06-18 [2]
   edgeR                  3.32.1     2021-01-14 [1]
   ellipsis               0.3.2      2021-04-29 [2]
   evaluate               0.14       2019-05-28 [2]
   fansi                  0.5.0      2021-05-25 [2]
   farver                 2.1.0      2021-02-28 [2]
   fastmap                1.1.0      2021-01-25 [2]
   fastmatch              1.1-3      2021-07-23 [1]
   fgsea                * 1.16.0     2020-10-27 [1]
   fitdistrplus           1.1-6      2021-09-28 [2]
   forcats              * 0.5.1      2021-01-27 [2]
   foreach                1.5.1      2020-10-15 [2]
   fs                     1.5.0      2020-07-31 [2]
   future               * 1.22.1     2021-08-25 [2]
   future.apply           1.8.1      2021-08-10 [2]
   genefilter             1.72.1     2021-01-21 [1]
   geneplotter            1.68.0     2020-10-27 [1]
   generics               0.1.1      2021-10-25 [2]
   GenomeInfoDb         * 1.26.7     2021-04-08 [1]
   GenomeInfoDbData       1.2.4      2021-04-15 [1]
   GenomicAlignments      1.26.0     2020-10-27 [1]
   GenomicRanges        * 1.42.0     2020-10-27 [1]
   GetoptLong             1.0.5      2020-12-15 [1]
   ggbeeswarm             0.6.0      2017-08-07 [1]
   ggplot.multistats    * 1.0.0      2019-10-28 [1]
   ggplot2              * 3.3.5      2021-06-25 [1]
   ggrepel                0.9.1      2021-01-15 [2]
   ggridges               0.5.3      2021-01-08 [2]
   git2r                  0.28.0     2021-01-10 [1]
   glmmTMB                1.1.2.3    2021-09-20 [1]
   GlobalOptions          0.1.2      2020-06-10 [1]
   globals                0.14.0     2020-11-22 [2]
   glue                   1.4.2      2020-08-27 [2]
   goftest                1.2-3      2021-10-07 [2]
   gplots                 3.1.1      2020-11-28 [2]
   gridExtra              2.3        2017-09-09 [2]
   gtable                 0.3.0      2019-03-25 [2]
   gtools                 3.9.2      2021-06-06 [2]
   here                   1.0.1      2020-12-13 [2]
   hexbin                 1.28.2     2021-01-08 [2]
   highr                  0.9        2021-04-16 [2]
   hms                    1.1.1      2021-09-26 [1]
   htmltools              0.5.2      2021-08-25 [2]
   htmlwidgets            1.5.4      2021-09-08 [2]
   httpuv                 1.6.3      2021-09-09 [2]
   httr                   1.4.2      2020-07-20 [2]
   ica                    1.0-2      2018-05-24 [2]
   igraph                 1.2.7      2021-10-15 [2]
   IRanges              * 2.24.1     2020-12-12 [1]
   irlba                  2.3.3      2019-02-05 [2]
   iterators              1.0.13     2020-10-15 [2]
   janitor                2.1.0      2021-01-05 [1]
   jquerylib              0.1.4      2021-04-26 [2]
   jsonlite               1.7.2      2020-12-09 [2]
   KernSmooth             2.23-20    2021-05-03 [2]
   knitr                  1.36       2021-09-29 [1]
   labeling               0.4.2      2020-10-20 [2]
   later                  1.3.0      2021-08-18 [2]
   lattice                0.20-45    2021-09-22 [2]
   lazyeval               0.2.2      2019-03-15 [2]
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   lifecycle              1.0.1      2021-09-24 [2]
   limma                  3.46.0     2020-10-27 [1]
   listenv                0.8.0      2019-12-05 [2]
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   lmerTest               3.1-3      2020-10-23 [1]
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   lubridate              1.8.0      2021-10-07 [2]
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   magrittr             * 2.0.1      2020-11-17 [1]
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   matrixStats          * 0.61.0     2021-09-17 [1]
   memoise                2.0.0      2021-01-26 [1]
   mgcv                   1.8-38     2021-10-06 [1]
   mime                   0.12       2021-09-28 [1]
   miniUI                 0.1.1.1    2018-05-18 [2]
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   numDeriv               2016.8-1.1 2019-06-06 [2]
   parallelly             1.28.1     2021-09-09 [2]
   patchwork              1.1.1      2020-12-17 [2]
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   pillar                 1.6.4      2021-10-18 [1]
   pkgbuild               1.2.0      2020-12-15 [1]
   pkgconfig              2.0.3      2019-09-22 [2]
   pkgload                1.2.3      2021-10-13 [2]
   plotly                 4.10.0     2021-10-09 [2]
   plyr                   1.8.6      2020-03-03 [2]
   png                    0.1-7      2013-12-03 [2]
   polyclip               1.10-0     2019-03-14 [2]
   prettyunits            1.1.1      2020-01-24 [2]
   processx               3.5.2      2021-04-30 [2]
   progress               1.2.2      2019-05-16 [2]
   promises               1.2.0.1    2021-02-11 [2]
   ps                     1.6.0      2021-02-28 [2]
   purrr                * 0.3.4      2020-04-17 [2]
   R.methodsS3            1.8.1      2020-08-26 [1]
   R.oo                   1.24.0     2020-08-26 [1]
   R.utils                2.11.0     2021-09-26 [1]
   R6                     2.5.1      2021-08-19 [2]
   RANN                   2.6.1      2019-01-08 [2]
   rappdirs               0.3.3      2021-01-31 [2]
   RColorBrewer         * 1.1-2      2014-12-07 [2]
   Rcpp                   1.0.7      2021-07-07 [1]
   RcppAnnoy              0.0.19     2021-07-30 [1]
   RCurl                  1.98-1.5   2021-09-17 [1]
   readxl               * 1.3.1      2019-03-13 [2]
   registry               0.5-1      2019-03-05 [1]
   remotes                2.4.1      2021-09-29 [1]
   reshape2               1.4.4      2020-04-09 [2]
   reticulate           * 1.22       2021-09-17 [2]
   rjson                  0.2.20     2018-06-08 [1]
   rlang                  0.4.12     2021-10-18 [2]
   rmarkdown              2.11       2021-09-14 [1]
   ROCR                   1.0-11     2020-05-02 [2]
   rpart                  4.1-15     2019-04-12 [2]
   rprojroot              2.0.2      2020-11-15 [2]
   Rsamtools              2.6.0      2020-10-27 [1]
   RSQLite                2.2.8      2021-08-21 [1]
   rsvd                   1.0.5      2021-04-16 [1]
   rtracklayer            1.50.0     2020-10-27 [1]
   Rtsne                  0.15       2018-11-10 [2]
   S4Vectors            * 0.28.1     2020-12-09 [1]
   sass                   0.4.0      2021-05-12 [2]
   scales               * 1.1.1      2020-05-11 [2]
   scater                 1.18.6     2021-02-26 [1]
   scattermore            0.7        2020-11-24 [2]
   sctransform            0.3.2      2020-12-16 [2]
   scuttle                1.0.4      2020-12-17 [1]
   seriation            * 1.3.1      2021-10-16 [1]
   sessioninfo            1.1.1      2018-11-05 [1]
   Seurat               * 4.0.5      2021-10-17 [2]
   SeuratObject         * 4.0.2      2021-06-09 [2]
   shape                  1.4.6      2021-05-19 [1]
   shiny                  1.7.1      2021-10-02 [2]
   SingleCellExperiment * 1.12.0     2020-10-27 [1]
   snakecase              0.11.0     2019-05-25 [1]
   sparseMatrixStats      1.2.1      2021-02-02 [1]
   spatstat.core          2.3-0      2021-07-16 [2]
   spatstat.data          2.1-0      2021-03-21 [2]
   spatstat.geom          2.3-0      2021-10-09 [2]
   spatstat.sparse        2.0-0      2021-03-16 [2]
   spatstat.utils         2.2-0      2021-06-14 [2]
   stringi                1.7.4      2021-08-25 [1]
   stringr              * 1.4.0      2019-02-10 [2]
   SummarizedExperiment * 1.20.0     2020-10-27 [1]
   survival               3.2-13     2021-08-24 [2]
   tensor                 1.5        2012-05-05 [2]
   testthat               3.1.0      2021-10-04 [2]
   tibble                 3.1.5      2021-09-30 [1]
   tidyr                  1.1.4      2021-09-27 [2]
   tidyselect             1.1.1      2021-04-30 [2]
   TMB                    1.7.22     2021-09-28 [1]
   TSP                    1.1-11     2021-10-06 [1]
   usethis                2.1.2      2021-10-25 [1]
   utf8                   1.2.2      2021-07-24 [1]
   uwot                   0.1.10     2020-12-15 [2]
   variancePartition      1.20.0     2020-10-27 [1]
   vctrs                  0.3.8      2021-04-29 [2]
   vipor                  0.4.5      2017-03-22 [1]
   viridis              * 0.6.2      2021-10-13 [1]
   viridisLite          * 0.4.0      2021-04-13 [1]
   whisker                0.4        2019-08-28 [1]
   withr                  2.4.2      2021-04-18 [2]
   workflowr            * 1.6.2      2020-04-30 [1]
   writexl              * 1.4.0      2021-04-20 [1]
   xfun                   0.27       2021-10-18 [1]
   XML                    3.99-0.8   2021-09-17 [1]
   xtable                 1.8-4      2019-04-21 [2]
   XVector                0.30.0     2020-10-27 [1]
   yaml                   2.2.1      2020-02-01 [2]
   zlibbioc               1.36.0     2020-10-27 [1]
   zoo                    1.8-9      2021-03-09 [2]
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[1] /pstore/home/macnairw/lib/conda_r3.12
[2] /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/R/library

 R -- Package was removed from disk.

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/libopenblasp-r0.3.12.so

locale:
 [1] LC_CTYPE=C                 LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [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] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] writexl_1.4.0               reticulate_1.22            
 [3] fgsea_1.16.0                BiocParallel_1.24.1        
 [5] ggplot.multistats_1.0.0     seriation_1.3.1            
 [7] ComplexHeatmap_2.6.2        SeuratObject_4.0.2         
 [9] Seurat_4.0.5                future_1.22.1              
[11] Matrix_1.3-4                SingleCellExperiment_1.12.0
[13] SummarizedExperiment_1.20.0 Biobase_2.50.0             
[15] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
[17] IRanges_2.24.1              S4Vectors_0.28.1           
[19] BiocGenerics_0.36.1         MatrixGenerics_1.2.1       
[21] matrixStats_0.61.0          purrr_0.3.4                
[23] readxl_1.3.1                forcats_0.5.1              
[25] ggplot2_3.3.5               scales_1.1.1               
[27] viridis_0.6.2               viridisLite_0.4.0          
[29] assertthat_0.2.1            stringr_1.4.0              
[31] data.table_1.14.2           magrittr_2.0.1             
[33] circlize_0.4.13             RColorBrewer_1.1-2         
[35] BiocStyle_2.18.1            colorout_1.2-2             
[37] workflowr_1.6.2            

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3            rtracklayer_1.50.0       
  [3] scattermore_0.7           R.methodsS3_1.8.1        
  [5] tidyr_1.1.4               bit64_4.0.5              
  [7] knitr_1.36                irlba_2.3.3              
  [9] DelayedArray_0.16.3       R.utils_2.11.0           
 [11] rpart_4.1-15              doParallel_1.0.16        
 [13] RCurl_1.98-1.5            generics_0.1.1           
 [15] callr_3.7.0               cowplot_1.1.1            
 [17] usethis_2.1.2             RSQLite_2.2.8            
 [19] RANN_2.6.1                bit_4.0.4                
 [21] spatstat.data_2.1-0       lubridate_1.8.0          
 [23] httpuv_1.6.3              xfun_0.27                
 [25] hms_1.1.1                 jquerylib_0.1.4          
 [27] evaluate_0.14             promises_1.2.0.1         
 [29] TSP_1.1-11                fansi_0.5.0              
 [31] progress_1.2.2            caTools_1.18.2           
 [33] igraph_1.2.7              DBI_1.1.1                
 [35] geneplotter_1.68.0        htmlwidgets_1.5.4        
 [37] spatstat.geom_2.3-0       ellipsis_0.3.2           
 [39] backports_1.2.1           dplyr_1.0.7              
 [41] annotate_1.68.0           deldir_1.0-6             
 [43] sparseMatrixStats_1.2.1   vctrs_0.3.8              
 [45] remotes_2.4.1             here_1.0.1               
 [47] Cairo_1.5-12.2            ROCR_1.0-11              
 [49] abind_1.4-5               cachem_1.0.6             
 [51] withr_2.4.2               sctransform_0.3.2        
 [53] GenomicAlignments_1.26.0  prettyunits_1.1.1        
 [55] goftest_1.2-3             cluster_2.1.2            
 [57] lazyeval_0.2.2            crayon_1.4.1             
 [59] genefilter_1.72.1         labeling_0.4.2           
 [61] edgeR_3.32.1              pkgconfig_2.0.3          
 [63] pkgload_1.2.3             vipor_0.4.5              
 [65] nlme_3.1-153              devtools_2.4.2           
 [67] blme_1.0-5                rlang_0.4.12             
 [69] globals_0.14.0            lifecycle_1.0.1          
 [71] miniUI_0.1.1.1            registry_0.5-1           
 [73] rsvd_1.0.5                cellranger_1.1.0         
 [75] rprojroot_2.0.2           polyclip_1.10-0          
 [77] lmtest_0.9-38             boot_1.3-28              
 [79] zoo_1.8-9                 beeswarm_0.4.0           
 [81] processx_3.5.2            whisker_0.4              
 [83] ggridges_0.5.3            GlobalOptions_0.1.2      
 [85] png_0.1-7                 rjson_0.2.20             
 [87] bitops_1.0-7              R.oo_1.24.0              
 [89] KernSmooth_2.23-20        Biostrings_2.58.0        
 [91] blob_1.2.2                DelayedMatrixStats_1.12.3
 [93] shape_1.4.6               parallelly_1.28.1        
 [95] beachmat_2.6.4            memoise_2.0.0            
 [97] plyr_1.8.6                hexbin_1.28.2            
 [99] ica_1.0-2                 gplots_3.1.1             
[101] zlibbioc_1.36.0           compiler_4.0.5           
[103] clue_0.3-60               lme4_1.1-27.1            
[105] DESeq2_1.30.1             fitdistrplus_1.1-6       
[107] cli_3.0.1                 Rsamtools_2.6.0          
[109] snakecase_0.11.0          XVector_0.30.0           
[111] lmerTest_3.1-3            listenv_0.8.0            
[113] ps_1.6.0                  patchwork_1.1.1          
[115] pbapply_1.5-0             TMB_1.7.22               
[117] MASS_7.3-54               mgcv_1.8-38              
[119] tidyselect_1.1.1          stringi_1.7.4            
[121] highr_0.9                 yaml_2.2.1               
[123] BiocSingular_1.6.0        locfit_1.5-9.4           
[125] ggrepel_0.9.1             muscat_1.5.1             
[127] sass_0.4.0                fastmatch_1.1-3          
[129] tools_4.0.5               future.apply_1.8.1       
[131] foreach_1.5.1             git2r_0.28.0             
[133] janitor_2.1.0             gridExtra_2.3            
[135] farver_2.1.0              Rtsne_0.15               
[137] digest_0.6.28             BiocManager_1.30.16      
[139] shiny_1.7.1               Rcpp_1.0.7               
[141] broom_0.7.9               scuttle_1.0.4            
[143] later_1.3.0               RcppAnnoy_0.0.19         
[145] httr_1.4.2                AnnotationDbi_1.52.0     
[147] colorspace_2.0-2          XML_3.99-0.8             
[149] fs_1.5.0                  tensor_1.5               
[151] splines_4.0.5             uwot_0.1.10              
[153] spatstat.utils_2.2-0      scater_1.18.6            
[155] sessioninfo_1.1.1         plotly_4.10.0            
[157] xtable_1.8-4              jsonlite_1.7.2           
[159] nloptr_1.2.2.2            testthat_3.1.0           
[161] R6_2.5.1                  pillar_1.6.4             
[163] htmltools_0.5.2           mime_0.12                
[165] glue_1.4.2                fastmap_1.1.0            
[167] minqa_1.2.4               BiocNeighbors_1.8.2      
[169] codetools_0.2-18          pkgbuild_1.2.0           
[171] utf8_1.2.2                lattice_0.20-45          
[173] bslib_0.3.1               spatstat.sparse_2.0-0    
[175] tibble_3.1.5              pbkrtest_0.5.1           
[177] numDeriv_2016.8-1.1       ggbeeswarm_0.6.0         
[179] colorRamps_2.3            leiden_0.3.8             
[181] gtools_3.9.2              magick_2.7.3             
[183] survival_3.2-13           limma_3.46.0             
[185] glmmTMB_1.1.2.3           rmarkdown_2.11           
[187] desc_1.4.0                munsell_0.5.0            
[189] GetoptLong_1.0.5          GenomeInfoDbData_1.2.4   
[191] iterators_1.0.13          variancePartition_1.20.0 
[193] reshape2_1.4.4            gtable_0.3.0             
[195] spatstat.core_2.3-0