Last updated: 2019-12-05

Checks: 7 0

Knit directory: reproducible_bioinformatics/

This reproducible R Markdown analysis was created with workflowr (version 1.5.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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    Ignored:    .Rhistory

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    Modified:   analysis/_site.yml

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File Version Author Date Message
Rmd 0b04728 davetang 2019-12-05 wflow_publish(files = "analysis/*.Rmd")

  • Tools like Conda and Docker simplify the installation of tools, which can be a major headache when tools have a long list of dependencies
  • Conda is a package management tool while Docker is a platform that can deliver software in packages called containers
  • Both tools can create isolated environments that can be easily shared with others so that others have an identical copy of your working space
    • Docker does this slightly better across different operating systems
  • The workflowr package provides a framework for promoting reproducible research
    • It creates a consistent directory structure that helps you stay organised
    • It seemlessly generates a website (that can be easily uploaded online) containing time-stamped, versioned, and documented results
    • It automatically performs various checks to ensure that your analysis was run in a clean environment
  • Follow these Ten Simple Rules for Reproducible Computational Research
  • At the very least, you should be able to understand and reproduce your work

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

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

[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.5.0 Rcpp_1.0.3      rprojroot_1.3-2 digest_0.6.22  
 [5] later_1.0.0     R6_2.4.1        backports_1.1.5 git2r_0.26.1   
 [9] magrittr_1.5    evaluate_0.14   stringi_1.4.3   rlang_0.4.1    
[13] fs_1.3.1        promises_1.1.0  whisker_0.4     rmarkdown_1.17 
[17] tools_3.6.1     stringr_1.4.0   glue_1.3.1      httpuv_1.5.2   
[21] xfun_0.11       yaml_2.2.0      compiler_3.6.1  htmltools_0.4.0
[25] knitr_1.26