Last updated: 2019-02-26

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Knit directory: dsc-log-fold-change/

This reproducible R Markdown analysis was created with workflowr (version 1.2.0). The Report tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 3351ce8

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    .sos/
    Ignored:    analysis/.sos/
    Ignored:    dsc/.sos/
    Ignored:    dsc/benchmark/
    Ignored:    output/

Untracked files:
    Untracked:  analysis/sim_power_berge_pbmc_results.Rmd
    Untracked:  dsc/dsc_test/
    Untracked:  dsc/modules/methodLatentFactor.dsc
    Untracked:  dsc/modules/methodsLatentFactor.R
    Untracked:  dsc/test.csv
    Untracked:  dsc/test.dsc

Unstaged changes:
    Modified:   dsc/benchmark.dsc
    Modified:   dsc/modules/dataSimulate.R
    Modified:   dsc/modules/dataSimulate.dsc

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 R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
html a85bfe7 jhsiao999 2018-11-15 add back htmls
Rmd 0cc76ea jhsiao999 2018-11-15 first commit
Rmd 2dd4a18 jhsiao999 2018-11-15 Start workflowr project.

The DSC code is available under the MIT license. The text, simulated data and figures are available under the CC-BY license.

Both of these allow you to reuse, adapt, or redistribute the content as long as you attribute us. If you use our data, please attribute us as follows:

The simulated data was generated by the Stephens lab at the University of Chicago (see https://github.com/stephenslab/dsc-log-fold-change for details).

If you use our code, please attribute us as follows:

The code used to process the data was adapted from the code written by the Stephens lab lab at the University of Chicago (see https://github.com/stephenslab/dsc-log-fold-change for details).