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Last updated: 2023-05-12

Checks: 2 0

Knit directory: NMD-analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). 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: bff9b8f

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The results in this page were generated with repository version bff9b8f. 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/Differential-transcript-usage.nb.html
    Ignored:    analysis/Enichment-analysis-fgsea.nb.html
    Ignored:    analysis/Enichment-analysis-goseq.nb.html

Untracked files:
    Untracked:  PCA.png
    Untracked:  PCA_plot.pdf
    Untracked:  PCA_transcript.png
    Untracked:  analysis/Differential-transcript-usage.Rmd
    Untracked:  analysis/UPF3B_KD.Rmd
    Untracked:  analysis/transcript-preprocessing.Rmd
    Untracked:  code/eisaR.R
    Untracked:  code/external_code/
    Untracked:  data/LTK_Sample Metafile_V3.txt
    Untracked:  data/Mus_musculus.GRCm39.105__nifs.tsv
    Untracked:  data/data.txt
    Untracked:  data/data2.txt
    Untracked:  data/fastqc/
    Untracked:  data/nif_output/
    Untracked:  data/samples.txt
    Untracked:  output/DEG-limma-results.Rda
    Untracked:  output/DEG-list.Rda
    Untracked:  output/DEG/
    Untracked:  output/EISA/
    Untracked:  output/ISAR/
    Untracked:  output/QC/
    Untracked:  output/Transcript/
    Untracked:  output/isoformSwitchAnalyzeR_isoform_AA_complete.fasta
    Untracked:  output/isoformSwitchAnalyzeR_isoform_AA_subset_1_of_3.fasta
    Untracked:  output/isoformSwitchAnalyzeR_isoform_AA_subset_2_of_3.fasta
    Untracked:  output/isoformSwitchAnalyzeR_isoform_AA_subset_3_of_3.fasta
    Untracked:  output/isoformSwitchAnalyzeR_isoform_nt.fasta
    Untracked:  output/limma-matrices.Rda
    Untracked:  tmp/

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   code/functions.R
    Modified:   code/libraries.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
html	bff9b8f	unawaz1996	2023-05-12	Build site.
html	f8ef81a	unawaz1996	2023-05-11	Build site.
html	8ecf3f0	unawaz1996	2023-05-11	Build site.
html	421e1d5	unawaz1996	2023-05-10	Build site.
html	401069b	unawaz1996	2023-05-04	Build site.
html	e8b5b16	unawaz1996	2023-05-04	Build site.
html	5196f41	unawaz1996	2023-04-21	Build site.
html	650317e	unawaz1996	2023-03-22	Build site.
html	1f4ee28	unawaz1996	2023-03-22	Build site.
html	109186b	unawaz1996	2023-03-22	Build site.
html	19b20b1	unawaz1996	2023-03-22	Build site.
html	a9a5164	unawaz1996	2023-03-14	Build site.
html	6b613fc	unawaz1996	2023-03-14	Build site.
html	780272b	unawaz1996	2023-03-14	Build site.
html	5a8cba6	unawaz1996	2023-03-14	Build site.
html	d5a71ed	unawaz1996	2023-03-14	Build site.
html	68d64c5	unawaz1996	2023-03-14	Build site.
Rmd	e7dde53	unawaz1996	2023-03-14	Start workflowr project.