lieberinstitute / recount3-docs

Documentation for all things related to `recount3`

recount3-docs

This GitHub repository is home to the recount3 documentation available at http://rna.recount.bio/. It consists of R Markdown files that generate the documentation website available at using the R package bookdown through a GitHub Actions workflow modified from biocthis. This GitHub repository also contains the code for making the recount3 study explorer using the R package shiny that you can view at shinyapps.io or embedded on the recount3 documentation website.

recount3-docs's Issues

URLs not loading

Hello,

Thanks for putting together such a great resource!

Via curl or my web browser I'm trying to access some of the URLs listed in this file and they are not loading.

https://github.com/LieberInstitute/recount3-docs/blob/master/docs/recount3_raw_project_files_with_default_annotation.csv

Here's an example url: http://idies.jhu.edu/recount3/data/human/data_sources/sra/gene_sums/65/SRP107565/sra.gene_sums.SRP107565.G026.gz

Unfortunately it looks like the file is unavailable. Have they moved or am I doing something wrong?

Any help is much appreciated!

Adding analysis related repos

Hi @KevinFYChen and @sjczheng,

I need your help adding the links to the GitHub repo(s) where you performed analyses related to recount3. Can you either point me to them or edit this file https://github.com/LieberInstitute/recount3-docs/blob/master/08_analysis.Rmd#L5?

It's ok if the repos are private right now as long as you plan to make them public once we publish the recount3 pre-print.

By the way, if you have any software-related repos we can list them at https://github.com/LieberInstitute/recount3-docs/blob/master/07_software.Rmd.

Thanks!

Best,
Leo

Checking with Sean & Eddie

Hi @metamaden, @eddieimada,

Am I missing any GitHub repos or project websites that you would like to list in either https://github.com/LieberInstitute/recount3-docs/blob/master/07_software.Rmd#L28 or https://github.com/LieberInstitute/recount3-docs/blob/master/08_analysis.Rmd?

It's becoming harder to keep track of where everything lives as the recount world keeps expanding :P

If I'm missing any links, please let me know or feel free to edit the files directly. The website will update automatically using GitHub actions.

Best,
Leo