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https://github.com/singha53-zz/omicsBioAnalytics
Omics BioAnalytics - RShiny web app for bioinformatics analyses
https://github.com/singha53-zz/omicsBioAnalytics
bioinformatics-analysis biomarkers multi-omics-data omics-bioanalytics shiny shinyapps
Last synced: 3 months ago
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Omics BioAnalytics - RShiny web app for bioinformatics analyses
- Host: GitHub
- URL: https://github.com/singha53-zz/omicsBioAnalytics
- Owner: singha53-zz
- Created: 2020-03-16T17:58:15.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-09-11T18:10:34.000Z (about 4 years ago)
- Last Synced: 2024-06-05T01:46:12.380Z (5 months ago)
- Topics: bioinformatics-analysis, biomarkers, multi-omics-data, omics-bioanalytics, shiny, shinyapps
- Language: R
- Homepage: https://amritsingh.shinyapps.io/omicsBioAnalytics/
- Size: 7.16 MB
- Stars: 8
- Watchers: 3
- Forks: 2
- Open Issues: 14
-
Metadata Files:
- Readme: README.Rmd
Awesome Lists containing this project
- jimsghstars - singha53-zz/omicsBioAnalytics - Omics BioAnalytics - RShiny web app for bioinformatics analyses (R)
README
---
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, cache = FALSE, warning = FALSE, message = FALSE)
```
**Omics BioAnalytics** is a Shiny app that perform common bioinformatics analyses such as descriptive analyses of demographics variables, exploratory data analysis, differential expression analysis and biomarker discovery analysis. The can either use the provided sample data to run through the various analyses of the app or upload their own data (demographics variables, omics data).
## Installing
- assuming R is installed.
```r
install.packages("devtools")
devtools::install_github("singha53/omicsBioAnalytics")
```
## Get started
- Step 1) add inst/app/makeEnvVars.R with the following contents (.Renvion worked locally but not on shinyapps.io):
```r
saveRDS("your-s3-bucket-name", "S3BUCKET.rds")
saveRDS("your-aws-access-key", "AWS_ACCESS_KEY_ID.rds")
saveRDS("your-aws-secret-access-key", "AWS_SECRET_ACCESS_KEY.rds")
saveRDS("your-aws-region", "AWS_DEFAULT_REGION.rds")
saveRDS("your-dynamodb-table-name", "TABLE_NAME.rds")
```
> The above script is sourced in global.R and the env are set locally and on shinyapps.io at runtime.
- Step 2) run the Shiny webapp
```r
library(omicsBioAnalytics);
omicsBioAnalytics::start_app()
```
## Programming/Scripting Languages
### Web-app
- RShiny (v3.6.1)
- RStudio (v1.2.5019)
### Multi-model app
- [Omics BioAnalytics Alexa Skill](https://github.com/singha53/omics-bioanalytics-alexa-skill)
## Sample datasets used for this app
### COVID-19 case study
#### How to use?
```r
library(omicsBioAnalytics);
data(covid19)
```
#### How to generate?
[steps to reproduce the COVID-19 data](https://github.com/singha53/omicsBioAnalytics/blob/master/inst/extdata/covid19/covid19.md)
### Heart Failure case study
#### How to use?
```r
library(omicsBioAnalytics);
data(heartFailure)
```
#### How to generate?
[steps to reproduce the heart failure data](https://github.com/singha53/omicsBioAnalytics/blob/master/inst/extdata/heartFailure/heartFailure.md)
### Pathway datasets
#### How to use?
```r
library(omicsBioAnalytics);
data(pathwayDB)
```
#### How to generate?
[steps to reproduce the pathway database](https://github.com/singha53/omicsBioAnalytics/blob/master/inst/extdata/pathwayDB/pathways.md)
## Features
- analyze multiple omics data obtained on the same set of subjects (samples/observations)
- interactive visualizations (heatmaps, networks, statistical graphs)
- RShiny app as an R-package
- voice-enabled analytics using an Alexa Skill
## Room for improvements
- use of Shiny modules to improve server-side code
- use of R6Class to improve code
## Contributing
If you'd like to contribute, please fork the repository and use a feature
branch. Pull requests are warmly welcome.
Note: if you build your own omicsBioAnalytics R-package and host it on your own github, then prior to deploying the app to shinyapps.io, make sure to restart your R session, then install the package from Github.
## Links
- Repository: https://github.com/singha53/omicsBioAnalytics/
## References
- [Shiny dashboard best practices](https://www.inwt-statistics.com/read-blog/best-practice-development-of-robust-shiny-dashboards-as-r-packages.html)
- [Cloudyr dynamodb orphaned R-library](https://github.com/cloudyr/aws.dynamodb)
## Copyright and license
Copyright 2020 AMRITPAL SINGH Inc.
The code in this project is licensed under MIT license.