Last updated: 2022-01-05

Checks: 7 0

Knit directory: single-cell-topics/analysis/

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Ignored files:
    Ignored:    data/droplet.RData
    Ignored:    data/pbmc_68k.RData
    Ignored:    data/pbmc_purified.RData
    Ignored:    data/pulseseq.RData
    Ignored:    output/droplet/diff-count-droplet.RData
    Ignored:    output/droplet/fits-droplet.RData
    Ignored:    output/droplet/rds/
    Ignored:    output/pbmc-68k/fits-pbmc-68k.RData
    Ignored:    output/pbmc-68k/rds/
    Ignored:    output/pbmc-purified/fits-pbmc-purified.RData
    Ignored:    output/pbmc-purified/rds/
    Ignored:    output/pulseseq/diff-count-pulseseq.RData
    Ignored:    output/pulseseq/fits-pulseseq.RData
    Ignored:    output/pulseseq/rds/
    Ignored:    output/sims/

Untracked files:
    Untracked:  analysis/de_analysis_detailed_look_cache/
    Untracked:  analysis/de_analysis_detailed_look_more_cache/
    Untracked:  plots/

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    Modified:   analysis/de_analysis_mast_deseq2.R
    Modified:   analysis/index.Rmd

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File Version Author Date Message
html e164b8f Peter Carbonetto 2022-01-05 Added link to overview page.
Rmd 3de0e0c Peter Carbonetto 2022-01-05 workflowr::wflow_publish(“index.Rmd”)

This is a more systematic comparison of the fastTopics DE analysis with MAST and DESeq2 based on an xinitial smaller simulation. The results were generated using the run_sims.R script, and here we summarize the results.


sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
# 
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# loaded via a namespace (and not attached):
#  [1] workflowr_1.6.2 Rcpp_1.0.7      rprojroot_1.3-2 digest_0.6.23  
#  [5] later_1.0.0     R6_2.4.1        backports_1.1.5 git2r_0.26.1   
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# [13] fs_1.3.1        promises_1.1.0  whisker_0.4     rmarkdown_2.3  
# [17] tools_3.6.2     stringr_1.4.0   glue_1.4.2      httpuv_1.5.2   
# [21] xfun_0.11       yaml_2.2.0      compiler_3.6.2  htmltools_0.4.0
# [25] knitr_1.26