Home

Last updated: 2024-10-09

Checks: 2 0

Knit directory: damsel_paper/analysis/

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: db488ae

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 db488ae. 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:    data/.DS_Store
    Ignored:    renv/library/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  code/helper-vissers.R
    Untracked:  data/damsel_counts.rds
    Untracked:  data/damsel_counts_a.rds
    Untracked:  data/damsel_counts_b.rds
    Untracked:  data/sd_1_SRR794884-vs-Dam.kde-norm.gatc-FDR0.01.peaks.gff
    Untracked:  data/sd_2_SRR7948877-vs-Dam.kde-norm.gatc-FDR0.01.peaks.gff
    Untracked:  data/txdb_genes.rds
    Untracked:  output/damsel_dm.rds
    Untracked:  output/damsel_genes.rds
    Untracked:  output/damsel_peaks.rds
    Untracked:  output/fp_vissers_peaks.txt
    Untracked:  output/keep
    Untracked:  output/lrt_sd.txt
    Untracked:  output/marshall_peaks.rds
    Untracked:  output/peaks.txt
    Untracked:  output/vissers_dm.rds
    Untracked:  output/vissers_peaks.rds
    Untracked:  output/vissers_peaks.txt
    Untracked:  output/vissers_peaks_mod.rds
    Untracked:  outputvenn_plot.png
    Untracked:  renv/.gitignore

Unstaged changes:
    Modified:   analysis/compare_genes.Rmd
    Modified:   code/run-Damsel.R
    Modified:   code/run-Vissers.R
    Modified:   renv.lock

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	db488ae	caitlinpage	2024-10-09	wflow_publish("index.Rmd")
html	d24b8ad	caitlinpage	2024-10-02	Build site.
Rmd	8a65d9f	caitlinpage	2024-10-02	wflow_publish("analysis/index.Rmd")
html	9d65b1a	caitlinpage	2024-10-02	Build site.
Rmd	6654a4f	caitlinpage	2024-10-02	wflow_publish("analysis/index.Rmd")
html	cf487bc	caitlinpage	2024-10-02	Build site.
Rmd	e761f85	caitlinpage	2024-10-02	wflow_publish("analysis/index.Rmd")
html	3ad67cf	caitlinpage	2024-10-02	Build site.
Rmd	e8a632e	caitlinpage	2024-10-02	wflow_publish("analysis/index.Rmd")
Rmd	554ccee	caitlinpage	2024-08-16	Start workflowr project.

Abstract DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to provide an end to end analysis for DamID sequencing data within R. Damsel performs quantification and testing of significant binding sites along with exploratory and visual analysis. Damsel produces results consistent with previous analysis approaches.

Home

Authors

Analysis