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The R Markdown file has staged 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.

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 e6f410c. 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:    .Rproj.user/
    Ignored:    ._.DS_Store
    Ignored:    analysis/20220707_TitrationSeries_DE_testing.nb.html
    Ignored:    code/.DS_Store
    Ignored:    code/._.DS_Store
    Ignored:    code/._DOCK7.pdf
    Ignored:    code/._DOCK7_DMSO1.pdf
    Ignored:    code/._DOCK7_SM2_1.pdf
    Ignored:    code/._FKTN_DMSO_1.pdf
    Ignored:    code/._FKTN_SM2_1.pdf
    Ignored:    code/._MAPT.pdf
    Ignored:    code/._PKD1_DMSO_1.pdf
    Ignored:    code/._PKD1_SM2_1.pdf
    Ignored:    code/.snakemake/
    Ignored:    code/5ssSeqs.tab
    Ignored:    code/Alignments/
    Ignored:    code/ChemCLIP/
    Ignored:    code/ClinVar/
    Ignored:    code/DE_testing/
    Ignored:    code/DE_tests.mat.counts.gz
    Ignored:    code/DE_tests.txt.gz
    Ignored:    code/Fastq/
    Ignored:    code/FastqFastp/
    Ignored:    code/Meme/
    Ignored:    code/OMIM/
    Ignored:    code/Session.vim
    Ignored:    code/SplicingAnalysis/
    Ignored:    code/featureCounts/
    Ignored:    code/log
    Ignored:    code/logs/
    Ignored:    code/scratch/
    Ignored:    data/._Hijikata_TableS1_41598_2017_8902_MOESM2_ESM.xls
    Ignored:    data/._Hijikata_TableS2_41598_2017_8902_MOESM3_ESM.xls
    Ignored:    output/._PioritizedIntronTargets.pdf

Untracked files:
    Untracked:  analysis/20220707_TitrationSeries_DE_testing.Rmd
    Untracked:  analysis/20220712_FitDoseResponseModels.Rmd

Unstaged changes:
    Modified:   analysis/20220629_FirstGlanceTitrationSeries.Rmd
    Modified:   analysis/index.Rmd

Staged changes:
    Modified:   analysis/20211216_DifferentialSplicing.Rmd
    New:        analysis/20220629_FirstGlanceTitrationSeries.Rmd
    Modified:   analysis/index.Rmd
    Modified:   code/Snakefile
    New:        code/config/samples.titrationseries.tsv
    New:        code/rules/ProcessTitrationSeries.smk
    New:        code/rules/RNASeqProcessing.smk
    Modified:   code/rules/common.smk
    New:        code/rules/pangolin.smk

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.