Rhea wiki
Discussion points
- What is the user story?
- What are the defined use cases?
- What sets Rhea apart from other similar efforts?
Road map
- Test current version with real-world data
- In the meantime: Plan future development
- Plan upstream API
- Interface with SRA
- Derive library params from data
- Plan user interaction (CLI, UI, website)
- Prepare for integration into web service?
- Discuss code organization, especially with respect to extending functionality
- Tools for individual samples
- Tools for multiple samples
- Tools for comparing groups of samples
- Discuss reuse and storage of results
- Minimize storage
- Minimize reruns
- How to determine whether samples have been run (database, folder structure, hashes)
- How to pass data between consecutive stages/pipelines (compare code organization)
- Plan downstream API
- How to extend MultiQC report?
- Snakemake report?
- Directory and file naming structure
- Prepare for integration into web service?
- Overall code organization
- How to coordinate different pipelines
- How to deal with interactive parts in between
- Plan upstream API
Other RNA-Seq analysis pipelines
Published
| date | name - link |
|---|---|
| 2017 | aRNApipe - https://academic.oup.com/bioinformatics/article/33/11/1727/2929343 |
| 2017 | RNACocktail - https://www.nature.com/articles/s41467-017-00050-4 |
| 2018 | VIPER - https://link.springer.com/article/10.1186/s12859-018-2139-9 |
| 2018 | hppRNA - https://academic.oup.com/bib/article-abstract/19/4/622/2918128 |
| 2019 | ARMOR - https://www.g3journal.org/content/9/7/2089 |
| 2019 | UTAP - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2728-2 |
| 2019 | BISR - https://link.springer.com/article/10.1186/s12859-019-3251-1 |
| 2019 | GEO2RNAseq - https://www.biorxiv.org/content/10.1101/771063v1 |
| 2019 | Shiny-Seq - https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4471-1 |
| https://github.com/nf-core/rnaseq |