Last updated: 2020-12-15

Checks: 2 0

Knit directory: 20201005_CF_Manuscript_Repo/

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.


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.

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 fa2a512. 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/

Untracked files:
    Untracked:  20200924_DEG_regulation_table.xlsx
    Untracked:  20201203_Pilot_PCA_CF_vs_Control.png
    Untracked:  20201203_Pilot_PCA_F508del_vs_Control.png
    Untracked:  20201203_Vali_PCA_CF_vs_Control.png
    Untracked:  20201203_Vali_Volcano_Plot_F508del_Control.png
    Untracked:  20201204_Pilot_PCA_CF_vs_Control.png
    Untracked:  20201214_CF_read_depth.csv
    Untracked:  20201214_CF_read_depth.xlsx
    Untracked:  20201214_Roast_Comparison_Pilot_and_Vali.html
    Untracked:  20201214_Roast_Validation_Comparison.html
    Untracked:  20201214_Vali_ASCL3_logCPM_F508del_Control.png
    Untracked:  20201214_Vali_CFTR_logCPM_F508del_Control.png
    Untracked:  20201214_Vali_FOXI1_logCPM_F508del_Control.png
    Untracked:  20201214_Validation_Top_Gene_Ontology_Terms.xlsx
    Untracked:  20201214_Validation_Volcano_Plot_F508del_Control.png
    Untracked:  20201214_Venn_Diagram_Pilot_Validation_DEGs.png
    Untracked:  20201215_Validation_DEGs.csv
    Untracked:  Rplot.png
    Untracked:  Rplot01.png
    Untracked:  Rplot02.png
    Untracked:  Rplot03.png
    Untracked:  Rplot04.png
    Untracked:  Rplot05.png
    Untracked:  Rplot06.png
    Untracked:  Rplot07.png
    Untracked:  Rplot08.png
    Untracked:  Rplot09.png
    Untracked:  Rplot10.png
    Untracked:  Rplot11.png
    Untracked:  Rplot12.png
    Untracked:  Rplot13.png
    Untracked:  Rplot14.png
    Untracked:  Rplot15.png
    Untracked:  Rplot16.png
    Untracked:  Rplot17.png
    Untracked:  Rplot18.png
    Untracked:  Rplot19.png
    Untracked:  Rplot20.png
    Untracked:  Rplot21.png
    Untracked:  Rplot22.png
    Untracked:  Rplot23.png
    Untracked:  Rplot24.png
    Untracked:  Rplot25.png
    Untracked:  Rplot26.png
    Untracked:  Rplot27.png
    Untracked:  SampleList.csv
    Untracked:  Supplemental Table 5_20201214_CF_Read_Depth_validation.xlsx
    Untracked:  Supplemental Table 5_20201214_CF_Read_Depth_validation.xlsx.csv
    Untracked:  Validation_Pilot_DEGs.csv
    Untracked:  alignlog.txt
    Untracked:  aln_stats.R
    Untracked:  aln_stats.csv
    Untracked:  code/CF_Manuscript_Functions.R
    Untracked:  code/ensemblToGenes.R
    Untracked:  data/Pilot_cohort_raw_counts_relabeled_for_upload_with_genes.txt
    Untracked:  data/Validation_cohort_raw_counts_relabeled_for_upload_with_genes.txt
    Untracked:  data/alignlog.txt
    Untracked:  data/chaperome_entrez.csv
    Untracked:  data/corrected_vali_counts.txt
    Untracked:  data/corrected_vali_counts_with_genes.txt
    Untracked:  data/ncbi_genes.txt
    Untracked:  ensembl_id_and_gene_names.txt
    Untracked:  filtered_genes.txt
    Untracked:  gene_counts.csv
    Untracked:  github_md.Rmd
    Untracked:  github_md.md
    Untracked:  github_md_files/
    Untracked:  htseq.all.counts.txt
    Untracked:  new_vali_sig_genes.txt
    Untracked:  old_new_gene_comp.R
    Untracked:  old_vali_counts_v1.txt
    Untracked:  old_vali_counts_v2.txt
    Untracked:  original_vali_genes.txt
    Untracked:  roast_comparison.Rmd
    Untracked:  up_down_genes.csv
    Untracked:  vali_counts_halved.txt

Unstaged changes:
    Deleted:    .Rprofile
    Deleted:    .gitattributes
    Modified:   .gitignore
    Deleted:    analysis/about.Rmd
    Deleted:    analysis/license.Rmd
    Deleted:    code/README.md

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 f7881c3 basilkhuder 2020-10-05 Build site.
Rmd 958c5ca basilkhuder 2020-10-05 wflow_publish(“analysis/index.Rmd”)
html 159b50b Basil Khuder 2020-10-01 Build site.
Rmd 338f3eb Basil Khuder 2020-10-01 Homepage contains all manuscript authors and proper correspondence
html 7811b5c Basil Khuder 2020-09-23 Build site.
html 1e4c88a Basil Khuder 2020-09-23 Build site.
html ae0426c Basil Khuder 2020-09-23 Build site.
html 570fd70 Basil Khuder 2020-09-23 Build site.
html 73b6507 Basil Khuder 2020-09-23 Build site.
Rmd a8928bf Basil Khuder 2020-09-23 wflow_publish("analysis/*")
html 522ce4d Basil Khuder 2020-09-23 Build site.
Rmd 53d3b3a Basil Khuder 2020-09-23 wflow_publish("analysis/*")
Rmd ad7c5cc Basil Khuder 2020-09-23 Start workflowr project.

The Proteostatic Network Chaperome is Downregulated in F508del Homozygote Cystic Fibrosis

Marc A. Sala1★, Michael Alexander 1★, Basil Khuder1, Yuliya Politanska1, Hiam Abdala-Valencia1, G.R. Scott Budinger1, Jing Liu1, Manu Jain1#†, Paul A. Reyfman1†

1 Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA.
Co-first authors contributed equally
Co-senior authors contributed equally
# Correspondence should be addressed to Manu Jain ()

This is the repository for all data, scripts and figures associated with this manuscript.