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Last updated: 2025-08-22

Checks: 2 0

Knit directory: DXR_continue/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). 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: c146c0a

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 c146c0a. 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:    data/Cormotif_data/
    Ignored:    data/DER_data/
    Ignored:    data/alignment_summary.txt
    Ignored:    data/all_peak_final_dataframe.txt
    Ignored:    data/cell_line_info_.tsv
    Ignored:    data/full_summary_QC_metrics.txt
    Ignored:    data/number_frag_peaks_summary.txt

Untracked files:
    Untracked:  code/corMotifcustom.R
    Untracked:  code/making_analysis_file_summary.R

Unstaged changes:
    Modified:   analysis/final_analysis.Rmd
    Modified:   analysis/multiQC_cut_tag.Rmd

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	c146c0a	reneeisnowhere	2025-08-22	new index
html	53071c5	reneeisnowhere	2025-08-13	Build site.
Rmd	a91d0d3	reneeisnowhere	2025-08-13	wflow_publish("analysis/index.Rmd")
html	6217e5f	reneeisnowhere	2025-08-13	Build site.
Rmd	08e39e0	reneeisnowhere	2025-08-13	wflow_publish("analysis/index.Rmd")
html	1b3c7c0	reneeisnowhere	2025-08-13	Build site.
Rmd	1647a39	reneeisnowhere	2025-08-13	wflow_publish(c("analysis/index.Rmd", "analysis/test.Rmd"))
html	f568652	reneeisnowhere	2025-08-13	Build site.
Rmd	293550c	reneeisnowhere	2025-08-13	update links
html	aa92650	reneeisnowhere	2025-08-12	Build site.
html	0f14098	reneeisnowhere	2025-08-12	Build site.
Rmd	fbbfcf1	reneeisnowhere	2025-08-12	updates
html	1f6414a	reneeisnowhere	2025-08-12	Build site.
Rmd	315ea39	reneeisnowhere	2025-08-12	wflow_publish("analysis/index.Rmd", view = FALSE, verbose = TRUE)
html	945f9c4	infurnoheat	2025-08-01	Build site.
Rmd	60816c4	infurnoheat	2025-08-01	wflow_publish("analysis/index.Rmd")
html	6d73378	infurnoheat	2025-07-30	Build site.
Rmd	d40aedf	infurnoheat	2025-07-30	wflow_publish("analysis/index.Rmd")
html	bfcc217	infurnoheat	2025-07-22	Build site.
Rmd	0f4b810	infurnoheat	2025-07-22	wflow_publish("analysis/index.Rmd")
html	6b3198d	infurnoheat	2025-07-14	Build site.
Rmd	92ac9a7	infurnoheat	2025-07-14	wflow_publish("analysis/index.Rmd")
html	1131ab4	infurnoheat	2025-07-02	Build site.
Rmd	f436ea6	infurnoheat	2025-07-02	wflow_publish("analysis/index.Rmd")
html	11858ef	infurnoheat	2025-07-02	Build site.
Rmd	bb57299	infurnoheat	2025-07-02	wflow_publish("analysis/index.Rmd")
html	78f96c9	infurnoheat	2025-07-02	Build site.
Rmd	ccd6e14	infurnoheat	2025-07-02	wflow_publish("analysis/index.Rmd")
Rmd	018b5d3	infurnoheat	2025-07-01	Start workflowr project.

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QC and peak analysis

Region selection and Differential analysis