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Open Source Tools

FDA Jumpstart Scripts

Clinical study evaluations scripts used by the FDA in their JumpStart tool has been developed based on SDTM standard. The FDA contributed the JumpStart SAS scripts so these are available on the PhUSE repository for use.

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SASScriptsOutputs

RPact

The R package RPACT is a statistical program module, characterized as a comprehensive, validated software R package, that enables the simulation and analysis of parallel group designs with continuous, binary, and survival endpoint. RPACT can be downloaded per CRAN and will be available as open-source under LGPL3.

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RToolStatistics

Visual Define-XML Editor

A cross-platform desktop application which allows to edit and review Define-XML files in a convenient and efficient way. It fully supports CDISC Define-XML v2.0 and ARM 1.0 standards.

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JavaScript, Node.jsToolDefine

Pinnacle21 Community Edition

This tool supports various CDISC processes including the validation and creation of the define.xml. It's broadly used in the pharmaceutical industry and currently required by the Japanese authority PMDA.

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Java, JavaScriptToolDefine, CDISC

TidyCDISC

TidyCDISC is an R-Shiny app. The purpose of tidyCDISC is to easily create custom tables and figures from ADaM datasets.

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RToolProgramming, Outputs

SASUnit

SASUnit is a unit testing framework for SAS(TM)-programs. It can be used for the development, execution and automatic documentation of tests for SAS programs. SASUnit is written purely on the basis of SAS macros and a few shell commands.

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SASToolProgramming

Douhau Data Studio

Douhau Data Studio is a data browser desktop application for CDISC SDTM, and support both SAS XPORT v5 and CDISC Dataset-XML file format.

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R, TypeScriptToolVisualization

Spectre (Roland's SAS® Macros)

A complete clinical reporting engine is provided as Sprectre. It's a comprehensive macro framework. Additionally 244 useful utility macros are available.

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SASScriptsOutputs

SAS Macros by Scott Bass

Scott Bass has built up a (semi) large collection of utility macros over the years with 73 macros currently. These are put up on GitHub to make them available for anyone. Almost all are utility in nature, and not tied to any particular project.

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SASScriptsProgramming

SASjs Core Macros

Much quality. Many standards. The Macro Core library exists to save time and development effort! Herein ye shall find a veritable host of production quality SAS macros. These are a mix of tools, utilities, functions and code generators that are useful in the context of Application Development on the SAS platform. Contributions are welcomed.

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SASScriptsProgramming

Reindeer - Result Render Tool

Reindeer is a VBA tool to render SAS results in LISTING, RTF, TAGSETS.RTF and Figures into a Word template file. PDF can be generated as well. This easy to use and very intuitive open source tool is sponsored by ClinStat.

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VBA, SASToolOutputs

Web Codebook

The web codebook is a JavaScript library that provides a concise summary of every variable in a dataset. The codebook includes interactive features such as real-time filters and requires minimal user configuration. When the page loads, the user sees a "codebook" providing a graphical data summary for each data column. It can be started trough R as well.

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JavaScript, RToolVisualization

PhUSE White Paper Central Tendencies Scripts

PhUSE has developed analysis and display white papers covering many aspects of clinical study evaluations. Additionally people developed corresponding R and SAS scripts which create the white paper outputs and graphics. These scripts are made publicy available in the PhUSE script repository.

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R, SASScriptsOutputs

StatTag

StatTag is a free plug-in for conducting reproducible research and creating dynamic documents using Microsoft Word with the R, Stata and SAS statistical packages.

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Word, Stata, R, SASToolOutputs

RTables

The RTables R package is a prototype to create and display complex tables with R. The cells in an RTable may contain any high-dimensional data structure which can then be displayed with cell-specific formatting instructions. Currently, RTables can be outputted in ascii and html.

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RToolOutputs

ggcharts

The ggcharts R package is a toolkit to easily generate visualizations which would otherwise need quite some lines of data manipluations and ggplot2 usage.

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RToolOutputs

Chris's SAS Macros

This is the SAS Macro collection from Chris Swenson who published 83 supporting SAS macros which can be used for various purposes.

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SASToolProgramming

R for Clinical Trials - Link List

A huge tool collection list for R exists and is maintained by Ed Zhang and Harry G. Zhang.

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RLinkProgramming

R4DSXML

R4DSXML is R package for import CDISC Dataset-XML and Define-XML as R data frame. The tool support CDISC Dataset-XML 1.0, Define-XML 2.0 and Analysis Results Metadata 1.0.

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RToolDefine

Smart Submission Dataset Viewer

Smart Submission Dataset Viewer is a Java-based viewer for CDISC submission files in the new Dataset-XML format. The newer versions also allow to generate Dataset-XML files starting from SAS-XPT files on the fly.

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JavaToolDefine

DefineXML SAS XMLMAP

The CDISC-Define-XML-SAS-XMLMAP provides two mapping files which can be used in SAS to map ODM and define.xml in version 2.0.0 to SAS dataets. Furthermore a macro is provided to create define-view like datasets in SAS.

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SASToolDefine

Data Visualization - SAS Blog

SAS has a blog post where various topics are discussed and examples are provided. The 'Data Visualization' blog contains a lot of examples including source code on various graphic types.

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SASScriptsVisualization

RhoInc Plots

Multiple Plot SAS Macros are made available by RhoInc employees in different GitHub subpages. There is a violin plot, sankey barchart, bee swarm and other related macros available.

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SASScriptsVisualization

safetyGraphics

SafetyGraphics - Clinical Trial Safety Graphics with R. This package provides a framework for evaluation of clinical trial safety in R. It includes several safety-focused visualizations to empower clinical data monitoring.

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JavaScript, RToolVisualization

Safety Histogram

Safety Histogram is a JavaScript library built with Webcharts (1, 2) that creates an interactive histogram plotting the distribution of lab measures, vital signs, and other measures related to safety in clinical trials.

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JavaScriptToolVisualization

Adverse Event Explorer

The AE Explorer is a JavaScript library that allows users to dynamically query adverse event (AE) data in real time. The default view is a single-screen display of AEs grouped by the MedDRA System Organ Class. Dot plots portray the incidence in the different treatment groups.

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JavaScriptToolVisualization

Clinical Timelines

Clinical Timelines is a JavaScript library that visualizes events over time via a faceted, interactive timeline chart. While initially designed for use in clinical trial research, the library works with any longitudinal data of one record per event.

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JavaScriptToolVisualization

CRF Heat Map

The CRF Heat Map visualizes the level of completeness of a clinical database by aggregating case report form (CRF) characteristics, such as the rate of CRFs entered, frozen, and locked and the number of unresolved queries.

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JavaScriptToolVisualization

Query Overview

Query Overview is a JavaScript library built using Webcharts (1, 2) that creates an interactive bar chart showing the distribution of queries that have been issued regarding data collected in a clinical trial.

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JavaScriptToolVisualization

Safety Results Over Time

Safety Results Over Time is a JavaScript library built using Webcharts (1, 2) that allows users to view summaries of clinical outcomes such as lab results and vital signs over time. A typical chart created with safety results over time.

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JavaScriptToolVisualization

Adverse Event Timelines

AE-timelines is a JavaScript library built using Webcharts (1, 2) that creates an adverse event timeline for each participant in a clinical trial. Clicking on the y-axis tick labels also opens an adverse event-level participant view.

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JavaScriptToolVisualization

Population Explorer

The Population Explorer is a simple JavaScript library that facilitates the real-time exploration of data sets using an intuitive user interface. The tool was designed to empower researchers to explore their medical research data in real time.

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JavaScriptToolVisualization

SMILE - Smart SAS Macros

This Smart SAS Macros - an Intuitive Library Extension contains small makros for example to download files from URLs or creating flat PDF navigation panes for ODS PDF.

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SASScriptsProgramming

Going Translational with Linked Data

In this project, formerly known as Clinical Trial Data to RDF, many scripts and macros are available to transform clinical trial data into linked data triples. There are also related scripts like visualization of triples and scripts (R and SAS) to triplify MedDRA.

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R, RDF, SASScriptsProgramming

PhUSE White Paper Utilities

24 utility macros mainly for testing and validation has been developed by a PhUSE Working Group to perform qualifications. These utilities are made available in the PhUSE Script Repository.

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SASScriptsProgramming

PhUSE Contributed Scripts & Macros

There are various scripts and macros available contributed to the PhUSE repository apart from those listed here as well. These might come from PhUSE working groups, individuals or presenters. Some are documented as PhUSE papers.

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R, SAS, OtherScripts

Others - Single Scripts & Macros

There are various scripts and macros available at single locations, these can be checked out under the 'programs' view.

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SASScripts