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.
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.
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
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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.