Merge pull request #2 from uab-cgds-worthey/dummy_for_PR

Review prior to public release

Author: gurpreet-bioinfo

.markdownlint.json

@@ -4,7 +4,7 @@
         "indent": 2
     },
     "MD013": {
-        "line_length": 120,
+        "line_length": 170,
         "tables": false
     }
 }

.test/README.md

@@ -5,81 +5,32 @@
 Markdown](https://github.com/uab-cgds-worthey/cgds_repo_template/actions/workflows/linting.yml/badge.svg)](https://github.com/uab-cgds-worthey/cgds_repo_template/actions/workflows/linting.yml)
 <!-- markdown-link-check-enable -->
 
-X-linked myopathy with excessive autophagy (XMEA) is caused by loss-of-function (LoF) pathogenic variants in the VMA21
+**Manuscript:** Multi-omics analysis identifies a novel *VMA21* gene variant that dysregulates RNA splicing causing rare
+X-linked myopathy with excessive autophagy
+
+X-linked myopathy with excessive autophagy (XMEA) is caused by loss-of-function (LoF) pathogenic variants in the *VMA21*
 gene on the X-chromosome. XMEA patients develop a progressive muscle weakness caused by an impaired autophagy process
 resulting in the accumulation of vacuoles within skeletal muscle, liver and neurons.
 
-* **Sashimi plot**
-  * [ggsashimi_analysis](./src/ggsashimi_analysis)
-* **Differential gene expression analysis**
-  * [dge_analysis](notebooks/dge)
-
 ## Requirements
 
-:pencil2: What are the requirements to install and run the project.
-
-## How to install
-
-:pencil2: Add installation instructions here.
-
-## How to run
-
-:pencil2: Add run instructions here. This includes necessary configurations as well as the commands used.
-
-## Repo's directory structure
+- [R](https://www.r-project.org/) version 4.2.3 (2023-03-15)
+- [Rstudio](https://posit.co/download/rstudio-desktop/) version 2023.03.0+386
+- [ggsashimi](https://github.com/guigolab/ggsashimi)
+- [DESeq2 R package](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
+- [ggplot2 R package](https://ggplot2.tidyverse.org/)
+- [EnhancedVolcano R package](https://github.com/kevinblighe/EnhancedVolcano)
 
-The directory structure below shows the nature of files/directories used in this repo.
+## Analysis code in the respective folders
 
-```sh
-$ tree -a cgds_repo_template/
-cgds_repo_template
-├── CHANGELOG.md      <- Log of changes made
-│
-├── CONTRIBUTING.md   <- Contribution guidelines
-│
-├── LICENSE.md        <- License for the repo
-│
-├── README.md
-│
-├── .gitignore        <- Specifies intentionally untracked files to ignore by git
-│
-├── .editorconfig     <- Helps maintain consistent coding styles for multiple users working on the same project across
-│                        various editors and IDEs. See https://editorconfig.org/ for more info
-│
-├── .markdownlint.json  <- Markdown linting config
-│
-├── .pylintrc         <- Python linting config
-│
-├── configs           <- Dir to store config files. Conda env, requirements.txt, etc.
-│
-├── data              <- Dir structure from http://drivendata.github.io/cookiecutter-data-science. Please give it a read.
-│   ├── external      <- Data from third party sources
-│   ├── interim       <- Intermediate data that has been transformed
-│   ├── processed     <- The final, canonical datasets and results
-│   └── raw           <- The original, immutable data dump
-│
-├── docs              <- Dir to store documentation.
-│
-├── notebooks         <- Dir to store Jupyter, R Markdown notebooks, etc.
-│
-├── src               <- Dir to store source code for use in this project
-│
-├── .github
-│   ├── ISSUE_TEMPLATE            <- Github issue templates
-│   │   ├── bug_report.md
-│   │   └── feature_request.md
-│   ├── PULL_REQUEST_TEMPLATE     <- Github PR templates
-│   │   └── pull_request_template.md
-│   └── workflows                 <- Github actions workflows for automated processes (eg. linting, etc)
-│       └── linting.yml
-│
-├── .test             <- Dir to store test datasets
-│   └── README.md
-│
-└── logs              <- Dir to store log files
+Scripts and notebooks utilized as part of this study are listed below. Please see them for files (gene annotation,
+etc.) necessary to run them successfully.
 
-```
+- **Splicing visualization via sashimi plot**
+  - [ggsashimi_analysis](./src/ggsashimi_analysis)
+- **Differential gene expression analysis**
+  - [dge_analysis](./src/dge_analysis)
 
-## Contributing
+## Manuscript preprint link
 
-We welcome contributions! [See the docs for guidelines](./CONTRIBUTING.md).
+- medRxiv: