zq2323/teal

Exploratory Web Apps for Analyzing Clinical Trial Data

Teal: Interactive Exploratory Data Analysis with Shiny Web-Applications

teal is a shiny-based interactive exploration framework for analyzing data. teal applications require app developers to specify:

• Data, which can be:
  • CDISC data, commonly used for clinical trial reporting
  • Independent datasets, for example from a data.frame
  • Related datasets, for example a set of data.frames with key columns to enable data joins
  • MultiAssayExperiment objects which are R data structures for representing and analyzing multi-omics experiments
• teal modules:
  • teal modules are shiny modules built within the teal framework that specify analysis to be performed. For example, it can be a module for exploring outliers in the data, or a module for visualizing the data in line plots. Although these can be created from scratch, lost of teal modules have been released and we recommend starting with modules found in the following packages:
    • teal.modules.general: general modules for exploring relational/independent/CDISC data
    • teal.modules.clinical: modules specific to CDISC data and clinical trial reporting
    • teal.modules.hermes: modules for analyzing MultiAssayExperiment objects

A lot of the functionality of the teal framework derives from the following packages:

• teal.data: creating and loading the data needed for teal applications.
• teal.widgets: shiny components used within teal.
• teal.slice: provides a filtering panel to allow filtering of data.
• teal.code: handles reproducibility of outputs.
• teal.transform: standardizes extracting and merging data.
• teal.logger: standardizes logging within teal framework.
• teal.reporter: allows teal applications to generate reports.

See these packages for more information about how to use the different parts of the teal framework.

Installation

For releases from August 2022 it is recommended that you create and use a Github PAT to install the latest version of this package. Once you have the PAT, run the following:

Sys.setenv(GITHUB_PAT = "your_access_token_here")
if (!require("remotes")) install.packages("remotes")
remotes::install_github("insightsengineering/teal@*release")

In order to run many of the examples you will also need to install the scda package.

A stable release of all NEST packages from June 2022 is also available here.

See package vignettes browseVignettes(package = "teal") for usage of this package.

Acknowledgment

This package is a result of a joint efforts by many developers and stakeholders. We would like to thank everyone who contributed so far!

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