Last updated: 2021-11-19

Checks: 2 0

Knit directory: invitroOA_pilot_repository/

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: b0e086c

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 b0e086c. 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:    .Rproj.user/

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 b0e086c Anthony Hung 2021-11-19 add qpcr
html 833430f Anthony Hung 2021-01-26 knit alsys files
html a35e0fb Anthony Hung 2021-01-26 knit alsys files
Rmd 62f071d Anthony Hung 2021-01-26 update index
html 62f071d Anthony Hung 2021-01-26 update index
Rmd 7221438 Anthony Hung 2021-01-26 add addiitonal figures for supplement
html b9d59c3 Anthony Hung 2021-01-21 knit analysis files
Rmd 78cfbcd Anthony Hung 2021-01-21 finish paring down files
Rmd e3fbd0f Anthony Hung 2021-01-21 add ward et al data files to data
html e3fbd0f Anthony Hung 2021-01-21 add ward et al data files to data
Rmd 0711682 Anthony Hung 2021-01-21 start normalization file
Rmd 99c70b8 Anthony Hung 2021-01-20 update external data
Rmd 28f57fa Anthony Hung 2021-01-19 Add files for analysis
Rmd bd30c9e Anthony Hung 2021-01-19 Start workflowr project.

Analysis of scRNA and bulk RNA sequencing data for “Characterizing gene expression responses to biomechanical strain in an in vitro model of osteoarthritis” project.

LCL-derived iPSCs from 3 Yoruba individuals were differentiated into mesenchymal stem cells and subsequently into chondrocytes. iPSC-derived chondrocytes were either placed under control conditions or treated with cyclic tensile strain for 24 hours (Total of 6 individual x treatment pairs). 3 technical replicates of the MSC-chondrocyte differentiation + strain/control treatment were conducted.Single cell RNAseq using the 10x platform was conducted for one replicate of the experiment (collection of one sample failed, meaning only 5 samples were single-cell sequenced). Bulk RNA sequencing was conducted for all 3 technical replicates.

If you are running the files in this repository to recreate the analyses, running them in the order they appear on this list is recommended.

Power Analysis