README.md

In Jasondd66/covid_19bioMarkers: Performs common bioinformatics analyses

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.

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):

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

library(omicsBioAnalytics);
omicsBioAnalytics::startApp()

Programming/Scripting Languages

Web-app

• RShiny (v3.6.1)
• RStudio (v1.2.5019)

Multi-model app

• Omics BioAnalytics Alexa Skill

Sample datasets used for this app

COVID-19 case study

How to use?

library(omicsBioAnalytics);
data(covid19)

How to generate?

steps to reproduce the COVID-19 data

Heart Failure case study

How to use?

library(omicsBioAnalytics);
data(heartFailure)

How to generate?

steps to reproduce the heart failure data

Pathway datasets

How to use?

library(omicsBioAnalytics);
data(pathwayDB)

How to generate?

steps to reproduce the pathway database

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
• Cloudyr dynamodb orphaned R-library

Copyright and license

Copyright 2020 AMRITPAL SINGH Inc.

The code in this project is licensed under MIT license.

Jasondd66/covid_19bioMarkers documentation built on Dec. 18, 2021, 12:33 a.m.