Add scripts for HPC Tumor-Normal-Differential-Expression analysis

[sangeetashukla]

Purpose/implementation Section

Create a new directory for deseq module with scripts compatible for HPC execution, and for Cavatica app creation/maintenance.

What scientific question is your analysis addressing?

Perform differential expression analysis for each pair of cancer histology type vs. all GTEX as well as each individual GTEX tissue (subgroup), where clinical data is available for 3 or more participants.

What was your approach?

• Develop a new module that uses the DESeq2 (R) package to perform this analysis.
• Develop scripts to create a Cavatica app, making the module functionality accessible with a more user-friendly GUI

What GitHub issue does your pull request address?

Issue 26

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

This module must be run on HPC or on Cavatica. Directions for the data that needs to be loaded is provided in the README.md

Which areas should receive a particularly close look?

For testing purposes, a new indices.txt file can be created, similar to the indices.txt that the run_Generate_Hist_GTEx_indices_file.sh execution will generate. This new file can have a smaller set of pairs of GTEx and Hist index values to run the differential expression analysis on.
Please let me know if more information is needed.

Is there anything that you want to discuss further?

Closing the previous PR, since the git repo and therefore feature branch had to be recreated.

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes. This module will generate all the expected result files in the expected formats.

Results

What types of results are included (e.g., table, figure)?

.tsv, .jsonl, and .rds files will be generated

What is your summary of the results?

This module allows user to conduct downstream visualization of tumor-normal different expression analysis using a choice of file formats, and on an interactive platform on Cavatica as well.

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[afarrel]

Great work @sangeetashukla. Thanks for working on this!

[runjin326]

Based on the discussion - we will be keeping separate docker so I will go ahead and merge it.

[sangeetashukla]

Based on the discussion - we will be keeping separate docker so I will go ahead and merge it.

Thank you @runjin326