README.md

In sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets

sendigR

The purpose of the sendigR package is to extract control data from a set of nonclinical studies stored in CDISC SEND format in a database to be used for cross study analysis.

sendigR includes:

• Functions to construct a relational database from any collection of SEND datasets;

• functions to query control data from database;

• An R Shiny application with a graphical user interface for facilitating cross-study analysis. Demo App can be found here.

• An optional Python package (xptclearner) to harmonize SEND datasets using SEND controlled terminology and extensible terminology;

Familiarity with the CDISC SEND data model and at least basic knowledge about animal studies is necessary to use the package.

Step by Step Installation

Installation of R and RStudio

R version 4.1.2 and above are used in developing and testing the sendigR.

R and RStudio Installation

Installation of Python and xptcleaner (optional)

Python version 3.9.6 and above are used in developing and testing the xptcleaner of sendigR. This is an optional component, you can skip this step if you will not use the xptcleaner to clean the xpt files.

Python installation

xptcleaner Python package installation

Installation of sendigR package

# Get CRAN version, this will be available soon
install.packages("sendigR")

# Or the development version from GitHub:
install.packages("devtools")
devtools::install_github('phuse-org/sendigR')

sendigR Usage

sendigR Overview

sendigR R Shiny Application

Using the sendigR xptcleaner

sendigR License

The sendigR package including the optional Python xptcleaner is subject to the MIT Open Source License:

MIT License

Copyright (c) 2022 PHUSE and BioCelerate

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE, ANY UPDATES TO THE SOFTWARE MADE BY CRAN, OR THE USE OR OTHER DEALINGS IN THE SOFTWARE OR ANY UPDATED VERSION.

Nothing in these scripts is intended to guide the analytic process and any interpretations of data found as a result of using these scripts are solely the responsibility of the user of the scripts and not the developers. All users are responsible for ensuring their own compliance with applicable laws, regulations, and agency guidance.

sendigR documentation built on Aug. 18, 2022, 9:07 a.m.