Last updated: 2021-05-21

Checks: 5 2

Knit directory: MS_lesions/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

The global environment had objects present when the code in the R Markdown file was run. These objects can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment. Use wflow_publish or wflow_build to ensure that the code is always run in an empty environment.

The following objects were defined in the global environment when these results were created:

Name Class Size
q function 1008 bytes

The command set.seed(20210118) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 1600da1. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rprofile
    Ignored:    .Rproj.user/
    Ignored:    ._.DS_Store
    Ignored:    ._MS_lesions.sublime-project
    Ignored:    MS_lesions.sublime-project
    Ignored:    MS_lesions.sublime-workspace
    Ignored:    analysis/.__site.yml
    Ignored:    analysis/ms02_doublet_id_cache/
    Ignored:    analysis/ms03_SampleQC_cache/
    Ignored:    analysis/ms04_conos_cache/
    Ignored:    analysis/ms05_splitting_cache/
    Ignored:    analysis/ms06_sccaf_cache/
    Ignored:    analysis/ms07_soup_cache/
    Ignored:    analysis/ms08_modules_cache/
    Ignored:    analysis/ms09_ancombc_cache/
    Ignored:    analysis/ms10_muscat_run01_cache/
    Ignored:    analysis/ms10_muscat_run02_cache/
    Ignored:    analysis/ms10_muscat_template_cache/
    Ignored:    analysis/ms11_paga_cache/
    Ignored:    analysis/ms12_markers_cache/
    Ignored:    analysis/supp06_sccaf_cache/
    Ignored:    code/muscat_plan.txt
    Ignored:    data/
    Ignored:    figures/
    Ignored:    output/

Untracked files:
    Untracked:  analysis/ms12_markers.Rmd
    Untracked:  code/dev_muscat_glmer_nb_20210510.R
    Untracked:  code/ms10_muscat_slurm_job.R
    Untracked:  code/ms10_muscat_slurm_job.slurm
    Untracked:  code/ms12_markers.R
    Untracked:  code/sketch_of_random_effects_20210430.R
    Untracked:  code/testing_lmer.R
    Untracked:  muscat_glmmtmb.err
    Untracked:  muscat_glmmtmb.out

Unstaged changes:
    Modified:   .gitignore
    Modified:   analysis/index.Rmd
    Modified:   analysis/ms07_soup.Rmd
    Modified:   analysis/ms09_ancombc.Rmd
    Modified:   analysis/ms10_muscat_template.Rmd
    Modified:   analysis/ms11_paga.Rmd
    Modified:   analysis/supp10_muscat.Rmd
    Modified:   code/ms00_utils.R
    Modified:   code/ms07_soup.R
    Modified:   code/ms09_ancombc.R
    Modified:   code/ms10_muscat_fns.R
    Modified:   code/ms10_muscat_runs.R
    Modified:   code/ms11_paga.R
    Modified:   code/supp10_muscat.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/supp10_muscat.Rmd) and HTML (docs/supp10_muscat.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html 9852840 Macnair 2021-05-12 Adding docs to repo for first time - massive!
Rmd 6dc6cc6 Macnair 2021-04-29 Updated muscat comparisons code
Rmd 129c53d Macnair 2021-04-16 Renamed a lot of things to add ms07_soup

Setup / definitions

Libraries

Helper functions

source('code/ms00_utils.R')
source('code/ms10_muscat_runs.R')
source('code/supp10_muscat.R')

Inputs

muscat_dir  = 'output/ms10_muscat'
wout_ls = list(
  tag    = 'run01',
  stamp  = '2021-05-06'
  )
with_ls = list(
  tag    = 'run09',
  stamp  = '2021-05-20'
  # tag    = 'run07',
  # stamp  = '2021-05-06'
  # tag    = 'run03',
  # stamp  = '2021-05-04'
  )

ls_ls     = list(wout = wout_ls, with = with_ls)
params_fs   = lapply(ls_ls, 
  function(ls) sprintf('%s/%s/muscat_params_%s_%s.rds', 
    muscat_dir, ls$tag, ls$tag, ls$stamp)
  )
res_fs    = lapply(ls_ls, 
  function(ls) sprintf('%s/%s/muscat_res_dt_%s_%s.txt.gz', 
    muscat_dir, ls$tag, ls$tag, ls$stamp)
  )

Outputs

Load inputs

ps_wout     = readRDS(params_fs[['wout']])
ps_with     = readRDS(params_fs[['with']])
res_wout    = load_results(res_fs[['wout']], ps_wout)
res_with    = load_results(res_fs[['with']], ps_wout)
if ('prop_rnd' %in% names(res_with)) {
  var_exp_dt  = load_var_exp(res_fs[['with']]) 
} else {
  var_exp_dt  = NULL
}
pb          = ps_wout$pb_f %>% readRDS %>% 
  .subset_pb(ps_wout$subset_spec)
  subsetting pb object
    restricting to samples that meet subset criteria
    updating factors to remove levels no longer observed
if (!is.null(ps_with$output_fs$mds_dist_f))
  mds_dist    = sprintf(ps_with$output_fs$mds_dist_f, with_ls$stamp) %>% 
    readRDS

Processing / calculations

comps_all   = merge(res_with, res_wout, 
  by = c('cluster_id', 'coef', 'test_var', 'gene_id', 'symbol'),
  suffixes = c('.with', '.wout'))
comps_dt    = comps_all[, .N, 
  by = .(cluster_id, coef, test_var, fc_cat.wout, fc_cat.with)]
p_cut       = 0.05
fc_cut      = 1
status_dt   = calc_status_dt(comps_all, p_cut, fc_cut)
ranks_dt    = calc_ranks_dt(status_dt, confounders, p_cut)
if (exists('mds_dist'))
  silh_dt     = calc_mds_silhouettes(mds_dist, pb)

Analysis

Heatmaps of fold changes with / without patient effect

for (cl in broad_ord) {
  cat('### ', cl, '\n')
  tmp_dt  = comps_all[cluster_id == cl]
  suppressWarnings(print(plot_comparison(tmp_dt, cl, what = 'fc')))
  cat('\n\n')
}

Oligodendrocytes

OPCs / COPs

Astrocytes

Microglia

Excitatory neurons

Inhibitory neurons

Endothelial cells

Pericytes

Immune

Heatmaps of p-values with / without patient effect

for (cl in broad_ord) {
  cat('### ', cl, '\n')
  tmp_dt  = comps_all[cluster_id == cl]
  suppressWarnings(print(plot_comparison(tmp_dt, cl, what = 'logp')))
  cat('\n\n')
}

Oligodendrocytes

OPCs / COPs

Astrocytes

Microglia

Excitatory neurons

Inhibitory neurons

Endothelial cells

Pericytes

Immune

Check genes that were lost / gained

cat('### Signif only without patient_id\n')

Signif only without patient_id

suppressWarnings(print(plot_sel_genes(ranks_dt, status_dt, pb, 'wout_rank')))

Version Author Date
9852840 Macnair 2021-05-12
cat('\n\n')
cat('### Signif only with patient_id\n')

Signif only with patient_id

suppressWarnings(print(plot_sel_genes(ranks_dt, status_dt, pb, 'with_rank')))

Version Author Date
9852840 Macnair 2021-05-12
cat('\n\n')

Genes with large / small patient effects

if (!is.null(var_exp_dt)) {
  cat('### Genes most affected by patients\n')
  suppressWarnings(print(plot_patient_genes(var_exp_dt, status_dt, pb, 'pat_high')))
  cat('\n\n')

  cat('### Genes least affected by patients\n')
  suppressWarnings(print(plot_patient_genes(var_exp_dt, status_dt, pb, 'pat_low')))
  cat('\n\n')
}

Distributions of patient variance %

if (!is.null(var_exp_dt))
  (plot_var_exp_vs_cpm(var_exp_dt))

Do samples cluster more by patient or by lesion?

if (exists('silh_dt')) {
  for (cl in broad_ord) {
    cat('### ', cl, '\n')
    suppressWarnings(print(plot_mds_silhouettes(silh_dt, cl)))
    cat('\n\n')
  }
}

Oligodendrocytes

Version Author Date
9852840 Macnair 2021-05-12

OPCs / COPs

Version Author Date
9852840 Macnair 2021-05-12

Astrocytes

Version Author Date
9852840 Macnair 2021-05-12

Microglia

Version Author Date
9852840 Macnair 2021-05-12

Excitatory neurons

Version Author Date
9852840 Macnair 2021-05-12

Inhibitory neurons

Version Author Date
9852840 Macnair 2021-05-12

Endothelial cells

Version Author Date
9852840 Macnair 2021-05-12

Pericytes

Version Author Date
9852840 Macnair 2021-05-12

Immune

Version Author Date
9852840 Macnair 2021-05-12

Do samples cluster more by patient or by lesion V2?

if (exists('silh_dt'))
  print(plot_mds_silhouettes_2(silh_dt))

Version Author Date
9852840 Macnair 2021-05-12

Outputs

devtools::session_info()
- Session info ---------------------------------------------------------------
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 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     2021-05-21                  

- Packages -------------------------------------------------------------------
 package              * version    date       lib
 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               0.3.1      2021-03-07 [1]
 Biobase              * 2.50.0     2020-10-27 [1]
 BiocGenerics         * 0.36.1     2021-04-16 [1]
 BiocManager            1.30.15    2021-05-11 [1]
 BiocNeighbors          1.8.2      2020-12-07 [1]
 BiocParallel         * 1.24.1     2020-11-06 [1]
 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                   1.2.1      2020-01-20 [2]
 boot                   1.3-28     2021-05-03 [2]
 broom                  0.7.6      2021-04-05 [2]
 bslib                  0.2.5      2021-05-12 [2]
 cachem                 1.0.5      2021-05-15 [2]
 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             * 0.4.12     2021-01-08 [1]
 cli                    2.5.0      2021-04-26 [2]
 clue                   0.3-59     2021-04-16 [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             2.0-1      2021-05-04 [2]
 ComplexHeatmap       * 2.6.2      2020-11-12 [1]
 crayon                 1.4.1      2021-02-08 [2]
 data.table           * 1.14.0     2021-02-21 [2]
 DBI                    1.1.1      2021-01-15 [2]
 dbplyr                 2.1.1      2021-04-06 [2]
 DelayedArray           0.16.3     2021-03-24 [1]
 DelayedMatrixStats     1.12.3     2021-02-03 [1]
 desc                   1.3.0      2021-03-05 [2]
 DESeq2                 1.30.1     2021-02-19 [1]
 devtools               2.4.1      2021-05-05 [1]
 digest                 0.6.27     2020-10-24 [2]
 doParallel             1.0.16     2020-10-16 [1]
 dplyr                * 1.0.6      2021-05-05 [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                  0.4.2      2021-01-15 [2]
 farver                 2.1.0      2021-02-28 [2]
 fastmap                1.1.0      2021-01-25 [2]
 fastmatch              1.1-0      2017-01-28 [1]
 fgsea                * 1.16.0     2020-10-27 [1]
 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                 1.21.0     2020-12-10 [2]
 future.apply           1.7.0      2021-01-04 [2]
 genefilter             1.72.1     2021-01-21 [1]
 geneplotter            1.68.0     2020-10-27 [1]
 generics               0.1.0      2020-10-31 [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]
 ggplot2              * 3.3.3      2020-12-30 [2]
 git2r                  0.28.0     2021-01-10 [1]
 glmmTMB                1.0.2.1    2020-07-02 [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]
 gplots                 3.1.1      2020-11-28 [2]
 gridExtra              2.3        2017-09-09 [2]
 grr                    0.9.5      2016-08-26 [1]
 gtable                 0.3.0      2019-03-25 [2]
 gtools                 3.8.2      2020-03-31 [2]
 haven                  2.4.1      2021-04-23 [2]
 highr                  0.9        2021-04-16 [2]
 hms                    1.1.0      2021-05-17 [2]
 htmltools              0.5.1.1    2021-01-22 [2]
 httpuv                 1.6.1      2021-05-07 [2]
 httr                   1.4.2      2020-07-20 [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]
 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                  1.33       2021-04-24 [1]
 later                  1.2.0      2021-04-23 [2]
 lattice                0.20-44    2021-05-02 [2]
 lifecycle              1.0.0      2021-02-15 [2]
 limma                * 3.46.0     2020-10-27 [1]
 listenv                0.8.0      2019-12-05 [2]
 lme4                   1.1-27     2021-05-15 [1]
 lmerTest               3.1-3      2020-10-23 [1]
 locfit                 1.5-9.4    2020-03-25 [1]
 lubridate              1.7.10     2021-02-26 [2]
 magrittr             * 2.0.1      2020-11-17 [1]
 MASS                   7.3-54     2021-05-03 [2]
 Matrix               * 1.3-3      2021-05-04 [2]
 Matrix.utils         * 0.9.8      2020-02-26 [1]
 MatrixGenerics       * 1.2.1      2021-01-30 [1]
 matrixStats          * 0.58.0     2021-01-29 [2]
 memoise                2.0.0      2021-01-26 [1]
 mgcv                   1.8-35     2021-04-18 [2]
 minqa                  1.2.4      2014-10-09 [1]
 modelr                 0.1.8      2020-05-19 [2]
 munsell                0.5.0      2018-06-12 [2]
 muscat               * 1.5.1      2021-04-15 [1]
 nlme                   3.1-152    2021-02-04 [2]
 nloptr                 1.2.2.2    2020-07-02 [1]
 numDeriv               2016.8-1.1 2019-06-06 [2]
 parallelly             1.25.0     2021-04-30 [2]
 patchwork            * 1.1.1      2020-12-17 [2]
 pbkrtest               0.5.1      2021-03-09 [1]
 pillar                 1.6.1      2021-05-16 [2]
 pkgbuild               1.2.0      2020-12-15 [1]
 pkgconfig              2.0.3      2019-09-22 [2]
 pkgload                1.2.1      2021-04-06 [2]
 plyr                   1.8.6      2020-03-03 [2]
 png                    0.1-7      2013-12-03 [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                2.10.1     2020-08-26 [1]
 R6                     2.5.0      2020-10-28 [2]
 RColorBrewer         * 1.1-2      2014-12-07 [2]
 Rcpp                   1.0.6      2021-01-15 [2]
 RCurl                  1.98-1.3   2021-03-16 [1]
 readr                * 1.4.0      2020-10-05 [2]
 readxl                 1.3.1      2019-03-13 [2]
 registry               0.5-1      2019-03-05 [1]
 remotes                2.3.0      2021-04-01 [1]
 reprex                 2.0.0      2021-04-02 [2]
 reshape2             * 1.4.4      2020-04-09 [2]
 rjson                  0.2.20     2018-06-08 [1]
 rlang                  0.4.11     2021-04-30 [2]
 rmarkdown            * 2.8        2021-05-07 [2]
 rprojroot              2.0.2      2020-11-15 [2]
 Rsamtools              2.6.0      2020-10-27 [1]
 RSQLite                2.2.7      2021-04-22 [1]
 rstudioapi             0.13       2020-11-12 [2]
 rsvd                   1.0.5      2021-04-16 [1]
 rtracklayer          * 1.50.0     2020-10-27 [1]
 rvest                  1.0.0      2021-03-09 [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]
 sctransform            0.3.2      2020-12-16 [2]
 scuttle                1.0.4      2020-12-17 [1]
 seriation            * 1.2-9      2020-10-01 [1]
 sessioninfo            1.1.1      2018-11-05 [1]
 shape                  1.4.5      2020-09-13 [2]
 SingleCellExperiment * 1.12.0     2020-10-27 [1]
 sparseMatrixStats      1.2.1      2021-02-02 [1]
 stringi                1.6.2      2021-05-17 [2]
 stringr              * 1.4.0      2019-02-10 [2]
 SummarizedExperiment * 1.20.0     2020-10-27 [1]
 survival               3.2-11     2021-04-26 [2]
 testthat               3.0.2      2021-02-14 [2]
 tibble               * 3.1.2      2021-05-16 [2]
 tictoc               * 1.0.1      2021-04-19 [1]
 tidyr                * 1.1.3      2021-03-03 [2]
 tidyselect             1.1.1      2021-04-30 [2]
 tidyverse            * 1.3.1      2021-04-15 [2]
 TMB                    1.7.20     2021-04-08 [1]
 TSP                    1.1-10     2020-04-17 [1]
 UpSetR               * 1.4.0      2019-05-22 [1]
 usethis                2.0.1      2021-02-10 [1]
 utf8                   1.2.1      2021-03-12 [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              * 0.6.1      2021-05-11 [1]
 viridisLite          * 0.4.0      2021-04-13 [2]
 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                   0.23       2021-05-15 [1]
 XML                    3.99-0.6   2021-03-16 [1]
 xml2                   1.3.2      2020-04-23 [2]
 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]
 source                            
 Bioconductor                      
 Bioconductor                      
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 4.0.3)                    
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 CRAN (R 4.0.2)                    
 CRAN (R 4.0.2)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.2)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Github (jalvesaq/colorout@79931fd)
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.2)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 4.0.3)                    
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.2)                    
 Bioconductor                      
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.0)                    
 Github (HelenaLC/muscat@c939663)  
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.2)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.2)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.3)                    
 CRAN (R 4.0.0)                    
 CRAN (R 4.0.0)                    
 Bioconductor                      
 CRAN (R 4.0.3)                    
 Bioconductor                      

[1] /pstore/home/macnairw/lib/conda_r3.12
[2] /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/R/library

sessionInfo()
R version 4.0.3 (2020-10-10)
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] cluster_2.1.2               ggbeeswarm_0.6.0           
 [3] rmarkdown_2.8               patchwork_1.1.1            
 [5] writexl_1.4.0               ComplexHeatmap_2.6.2       
 [7] fgsea_1.16.0                tictoc_1.0.1               
 [9] edgeR_3.32.1                limma_3.46.0               
[11] reshape2_1.4.4              scater_1.18.6              
[13] Matrix.utils_0.9.8          Matrix_1.3-3               
[15] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
[17] Biobase_2.50.0              MatrixGenerics_1.2.1       
[19] matrixStats_0.58.0          seriation_1.2-9            
[21] UpSetR_1.4.0                BiocParallel_1.24.1        
[23] muscat_1.5.1                dplyr_1.0.6                
[25] purrr_0.3.4                 readr_1.4.0                
[27] tidyr_1.1.3                 tibble_3.1.2               
[29] tidyverse_1.3.1             rtracklayer_1.50.0         
[31] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
[33] IRanges_2.24.1              S4Vectors_0.28.1           
[35] BiocGenerics_0.36.1         forcats_0.5.1              
[37] ggplot2_3.3.3               scales_1.1.1               
[39] viridis_0.6.1               viridisLite_0.4.0          
[41] assertthat_0.2.1            stringr_1.4.0              
[43] data.table_1.14.0           magrittr_2.0.1             
[45] circlize_0.4.12             RColorBrewer_1.1-2         
[47] BiocStyle_2.18.1            colorout_1.2-2             
[49] workflowr_1.6.2            

loaded via a namespace (and not attached):
  [1] R.methodsS3_1.8.1         bit64_4.0.5              
  [3] knitr_1.33                irlba_2.3.3              
  [5] DelayedArray_0.16.3       R.utils_2.10.1           
  [7] RCurl_1.98-1.3            doParallel_1.0.16        
  [9] generics_0.1.0            callr_3.7.0              
 [11] usethis_2.0.1             RSQLite_2.2.7            
 [13] future_1.21.0             bit_4.0.4                
 [15] xml2_1.3.2                lubridate_1.7.10         
 [17] httpuv_1.6.1              xfun_0.23                
 [19] hms_1.1.0                 jquerylib_0.1.4          
 [21] evaluate_0.14             promises_1.2.0.1         
 [23] TSP_1.1-10                fansi_0.4.2              
 [25] progress_1.2.2            caTools_1.18.2           
 [27] dbplyr_2.1.1              readxl_1.3.1             
 [29] DBI_1.1.1                 geneplotter_1.68.0       
 [31] ellipsis_0.3.2            backports_1.2.1          
 [33] annotate_1.68.0           sparseMatrixStats_1.2.1  
 [35] vctrs_0.3.8               remotes_2.3.0            
 [37] Cairo_1.5-12.2            cachem_1.0.5             
 [39] withr_2.4.2               grr_0.9.5                
 [41] sctransform_0.3.2         GenomicAlignments_1.26.0 
 [43] prettyunits_1.1.1         crayon_1.4.1             
 [45] genefilter_1.72.1         pkgconfig_2.0.3          
 [47] pkgload_1.2.1             nlme_3.1-152             
 [49] vipor_0.4.5               blme_1.0-5               
 [51] devtools_2.4.1            rlang_0.4.11             
 [53] globals_0.14.0            lifecycle_1.0.0          
 [55] registry_0.5-1            modelr_0.1.8             
 [57] rsvd_1.0.5                cellranger_1.1.0         
 [59] rprojroot_2.0.2           boot_1.3-28              
 [61] reprex_2.0.0              beeswarm_0.3.1           
 [63] processx_3.5.2            whisker_0.4              
 [65] GlobalOptions_0.1.2       png_0.1-7                
 [67] rjson_0.2.20              bitops_1.0-7             
 [69] R.oo_1.24.0               KernSmooth_2.23-20       
 [71] Biostrings_2.58.0         blob_1.2.1               
 [73] DelayedMatrixStats_1.12.3 shape_1.4.5              
 [75] parallelly_1.25.0         beachmat_2.6.4           
 [77] memoise_2.0.0             plyr_1.8.6               
 [79] gplots_3.1.1              zlibbioc_1.36.0          
 [81] compiler_4.0.3            clue_0.3-59              
 [83] lme4_1.1-27               DESeq2_1.30.1            
 [85] Rsamtools_2.6.0           cli_2.5.0                
 [87] XVector_0.30.0            lmerTest_3.1-3           
 [89] listenv_0.8.0             ps_1.6.0                 
 [91] TMB_1.7.20                MASS_7.3-54              
 [93] mgcv_1.8-35               tidyselect_1.1.1         
 [95] stringi_1.6.2             highr_0.9                
 [97] yaml_2.2.1                BiocSingular_1.6.0       
 [99] locfit_1.5-9.4            sass_0.4.0               
[101] fastmatch_1.1-0           tools_4.0.3              
[103] future.apply_1.7.0        rstudioapi_0.13          
[105] foreach_1.5.1             git2r_0.28.0             
[107] gridExtra_2.3             farver_2.1.0             
[109] digest_0.6.27             BiocManager_1.30.15      
[111] Rcpp_1.0.6                broom_0.7.6              
[113] scuttle_1.0.4             later_1.2.0              
[115] httr_1.4.2                AnnotationDbi_1.52.0     
[117] colorspace_2.0-1          rvest_1.0.0              
[119] XML_3.99-0.6              fs_1.5.0                 
[121] splines_4.0.3             sessioninfo_1.1.1        
[123] xtable_1.8-4              jsonlite_1.7.2           
[125] nloptr_1.2.2.2            testthat_3.0.2           
[127] R6_2.5.0                  pillar_1.6.1             
[129] htmltools_0.5.1.1         glue_1.4.2               
[131] fastmap_1.1.0             minqa_1.2.4              
[133] BiocNeighbors_1.8.2       codetools_0.2-18         
[135] pkgbuild_1.2.0            utf8_1.2.1               
[137] lattice_0.20-44           bslib_0.2.5              
[139] numDeriv_2016.8-1.1       pbkrtest_0.5.1           
[141] colorRamps_2.3            gtools_3.8.2             
[143] survival_3.2-11           glmmTMB_1.0.2.1          
[145] desc_1.3.0                munsell_0.5.0            
[147] GetoptLong_1.0.5          GenomeInfoDbData_1.2.4   
[149] iterators_1.0.13          variancePartition_1.20.0 
[151] haven_2.4.1               gtable_0.3.0