Last updated: 2021-05-26

Checks: 2 0

Knit directory: hesc-epigenomics/

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.

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: fcc223e

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 fcc223e. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/200510_chromosomes_extended.Rmd
    Ignored:    analysis/210413_bivalent_groups_extended.Rmd
    Ignored:    analysis/210518_gene_group_categories_extended.Rmd
    Ignored:    analysis/annotations_cache/
    Ignored:    analysis/annotations_extended.Rmd
    Ignored:    analysis/gene_set_analysis_extended.Rmd
    Ignored:    analysis/global_bins_extended.Rmd
    Ignored:    analysis/histone_marks_vs_expression_extended.Rmd
    Ignored:    analysis/kumar_2020_comparison_extended.Rmd
    Ignored:    analysis/messmer_2019_gene_groups_extended.Rmd
    Ignored:    data/bed/
    Ignored:    data/bw
    Ignored:    data/igv/
    Ignored:    data/liftover/
    Ignored:    data/meta/
    Ignored:    data/other/
    Ignored:    data/peaks
    Ignored:    data/rnaseq/

Untracked files:
    Untracked:  analysis/master_gene_table.Rmd
    Untracked:  code/heatmap_panels.R
    Untracked:  output/01_profiles.svg
    Untracked:  output/01_proportional_w_h2aub.svg
    Untracked:  output/01_proportional_w_h2aub_and_not_enriched_manual.svg
    Untracked:  output/01_proportional_w_h2aub_not_enriched.svg
    Untracked:  output/01_proportional_w_k4.png
    Untracked:  output/01_proportional_w_k4.svg
    Untracked:  output/01_sizes.svg
    Untracked:  output/Kumar_2020/
    Untracked:  output/gene_groups_k27_enriched_selected_by_shrunk_lfc.png
    Untracked:  output/gene_groups_k27_k4_enriched_plus_h2aub.png
    Untracked:  output/gene_groups_k27_k4_ni_enriched_selected_by_shrunk_lfc.png
    Untracked:  output/gene_groups_k27_up_subsets.png
    Untracked:  output/gene_groups_panel_by_k27.png
    Untracked:  output/gene_groups_panel_by_k27_regardless_k4_high_plus_h2aub.png
    Untracked:  output/gene_groups_panel_by_k4.png
    Untracked:  output/gene_groups_panel_only_k4_intersecting.png
    Untracked:  output/gene_groups_panel_only_k4_ni_high.png
    Untracked:  output/gene_groups_panel_only_k4_ni_high_plus_h2aub.png
    Untracked:  output/gene_groups_panel_only_k4_pr_high_plus_h2aub.png
    Untracked:  output/gene_groups_panel_w_k4.png
    Untracked:  output/gene_groups_panel_w_k4_enriched_naive.png
    Untracked:  output/gene_groups_panel_w_k4_naive.png
    Untracked:  output/h3k27m3_h2aub_panel_at_differential_k27_all_k4_enriched.png
    Untracked:  output/test_proportional.png

Unstaged changes:
    Modified:   analysis/annotations.Rmd
    Modified:   analysis/fig_01_quantitative_chip.Rmd
    Modified:   code/globals.R
    Modified:   code/ucsc_annotations.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/index.Rmd) and HTML (docs/index.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
Rmd 0f37941 cnluzon 2021-03-12 Fig1 fresh
html 0f37941 cnluzon 2021-03-12 Fig1 fresh
Rmd ef20c53 cnluzon 2021-03-11 Annotations
html ef20c53 cnluzon 2021-03-11 Annotations
html aa434ad cnluzon 2021-02-08 Per chromosome density report
Rmd eb48856 cnluzon 2021-02-08 wflow_publish(“analysis/”)
html 0437358 cnluzon 2021-02-07 Build site.
Rmd 8942fdf cnluzon 2021-02-07 Index page
html 8942fdf cnluzon 2021-02-07 Index page
Rmd 0481b52 cnluzon 2021-02-05 RNA seq first analysis
html 0481b52 cnluzon 2021-02-05 RNA seq first analysis
Rmd 87ff15f cnluzon 2021-02-05 Renamed read counts file
html 87ff15f cnluzon 2021-02-05 Renamed read counts file
html 7cafaa1 cnluzon 2021-02-03 Build site.
Rmd 930c015 cnluzon 2021-02-03 wflow_publish(“analysis/”)
html 331f00c cnluzon 2021-02-03 Build site.
Rmd 04408d2 cnluzon 2021-02-03 Global read counts
Rmd 897ecf5 cnluzon 2021-02-02 wflow_git_commit(all = TRUE)
Rmd 407fa20 cnluzon 2021-02-02 Start workflowr project.

Supplementary code and analysis for publication.

Publication figures

Supplementary analyses