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Hands On Clinical Reporting Using R

Курс от Genentech
Средний≈ 20.9 чАнглийский
О курсеНавыкиПрограммаПреподаватели

О курсе

The aim of this course is to introduce learners to open-source R packages that can be used to perform clinical data reporting tasks. The main emphasis of the course will be the clinical data flow from raw data (both CRF and non-CRF) to SDTM to ADaM to final outputs. While several open-source tools to complete these tasks will be introduced, the objective of this course is not to become an expert in any of these tools but rather to introduce participants to the broader concepts behind these tasks. That way the tools simply serve as an example of how the underlying concepts could be put into action in code.

Навыки, которые вы освоите

R ProgrammingClinical TrialsShiny (R Package)Interactive Data VisualizationStatistical ReportingData ModelingData ManipulationStatistical AnalysisStatistical ProgrammingClinical Data ManagementR (Software)Case Report FormsDrug DevelopmentData ScienceClinical ResearchData PreprocessingDashboardPharmaceuticalsData VisualizationData Presentation

Программа курса

8 модулей · 156 учебных материалов

01Hands On Clinical Reporting Using R3 материалов

Course Introduction

Welcome to Hands On Clinical Reporting Using R!ВидеоPre-requisite Reading: Why open-source tools?ЧтениеIntroductions and BackgroundОбсуждение
02Fundamentals8 материалов

Module Introduction

Учитесь у экспертов

Adrian Chan

Преподаватель курса

Tatiana Alonso Amor

Преподаватель курса

Stefan Pascal Thoma

Analytical Data Scientist

Joel Laxamana

Преподаватель курса

Leena Khatri

Преподаватель курса

Vincent Shen

Преподаватель курса

Jana Stoilova

Data Scientist

Hands On Clinical Reporting Using R
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Обучение на Coursera

≈ 20.9 ч

8 модулей

Язык: Английский

Субтитры: Арабский, Французский, Итальянский, Бразильский португальский, Корейский, Немецкий, Испанский, Японский, Венгерский

Часть программы вашего университета
Introduction FundamentalsВидео

Lesson 1 : Phase III Clinical Trials

Phase 3 Clinical Trials - Protocol & SAPВидео

Lesson 2: Data Collection

Data Collection - Using CRFs and Other MeansВидео

Lesson 3: Data Standards

CDISC SDTM and ADaM StandardsВидео

Lesson 4: FDA Submission Package

FDA(U.S.) Submission Package Видео

Lesson 5: Clinical Data Flow and Module Review

Clinical Data Flow: From Raw Data to Final OutputsВидео

Deciphering Clinical Trials: A Comprehensive Quiz on SAP, Estimands, and Data Standards

Deciphering Clinical Trials: A Comprehensive Quiz on SAP, Estimands, and Data StandardsЗадание

Unlocking the Data Puzzle: further reading on data Collection, Standards, and Health Authorities

Unlocking the Data Puzzle: further reading on data Collection, Standards, and Health AuthoritiesЧтение
03SDTM : Study Data Tabulation Model5 материалов

Lesson 1: Introduction

Introduction SDTMВидео

Lesson 2: Context and Workflow

Context and WorkflowВидео

Lesson 3: SDTM Data Mapping

SDTM Data MappingВидео

Lesson 4: Programming SDTM

Programming SDTMВидео

Mastering SDTM: A Quiz on Study Data Standards and Implementation

Mastering SDTM: A Quiz on Study Data Standards and ImplementationЗадание
04ADaM Transformations (Introductory)24 материалов

Module introduction

IntroductionВидео

Lesson 1: Introduction to ADaM

What is ADaM?ВидеоSubject-Level Analysis Dataset Structure (ADSL)ВидеоOccurrence Data Structure (OCCDS)ВидеоBasic Data Structure (BDS)ВидеоLesson One - Test your knowledgeЗаданиеSupplemental Resources on Understanding ADaM Standards in the IndustryЧтение

Lesson 2: What is Pharmaverse?

The VisionВидеоadmiral and pharmaverse for ADaM DevelopmentВидеоStoring and Using ADaM MetadataВидеоPart 1 - Metacore ObjectВидеоPart 2 - Metacore ObjectВидеоPart 3 - Metacore ObjectВидео

Lesson 3: Putting it all together

Part 1 - ADSL demoВидеоPart 2 - ADSL demoВидеоPart 3 - ADSL demoВидеоLesson Three - Test your knowledgeЗаданиеLinks on ADaM Documentation and Github Repos for Code Used in the DemosЧтение

Module Review

Module ReviewВидеоQuiz ResourcesЧтениеModule Quiz - ADaM Transformations (Introductory) using Pharmaverse R PackagesЗадание
05ADaM Transformations (Advanced)46 материалов

Module Intro : OCCDS - ADAE

Introduction to OCCDS and ADAEВидеоADAE Training OverviewВидео

Lesson 1 : OCCDS - ADAE Review

What to expect going into Session 1ВидеоAdverse Events backgroundВидеоLesson 1 : Test your knowledgeЗадание

Lesson 2 : Pharmaverse, Template Code Resource/Reference

R Packages, Tools and Resources for this training.ВидеоInstructions to Install R environment for the training demos ahead.ЧтениеLesson 2 : Test your knowledgeЗадание

Lesson 3 : Reading in Data, Derive/Impute datetimes, Relative Days, Durations

Getting started programming ADAE in RВидеоLet's read in the source dataВидеоConverting blanks to values to NAВидеоMerging in ADSL variablesВидеоDeriving Adverse Event Start datetimeВидеоDeriving Adverse Event End datetimeВидео

Lesson 4 : Date-time of Last Dose & AE Severity, Causality and Toxicity Grades

What to expect in Session 4ВидеоLast Dose datetimeВидеоHow to check Last Dose datetime derivationВидеоSeverity and CausalityВидеоLesson 4 : Test your knowledgeЗадание

Lesson 5 : Treatment-emergent AEs, Occurence Flags, Query variables

What will be covered in this Session?ВидеоFlagging Treatment-Emergent AEsВидеоTreatment-Emergent Flag windowВидеоFlagging AE OccurenceВидеоWhat are Standard MedDRA Queries (SMQs) and Custom Queries (CQs)?ВидеоDeriving Standard MedDRA Queries (SMQs) and Custom Queries (CQs)Видео

Lesson 6a : ADSL variables & Sequence numbers

What to expect in Session 6ВидеоAdding in ADSL variablesВидеоDeriving Analysis sequenceВидеоLesson 6a : Test your knowledgeЗадание

Lesson 6b : Var labels and attrs using {metacore}, {metatools}, & {xportr}

Reading in your ADaM specificationsВидеоChecking variables between your dataset and specificationsВидеоDropping unneeded variables from your datasetВидеоOrdering variables in your datasetВидеоSorting your dataset by the sort key per your specficationsВидеоVariable Length attributesВидео

ADaM Transformations (Advanced) Module Review

Module ReviewВидеоADAE Quiz ResourcesЧтениеQuiz - ADaM Transformations (Advanced) using Pharmaverse R PackagesЗадание
06Static TLGs (NEST)38 материалов

Module Introduction

Creating static TLGs for clinical reporting with RВидео

Lesson 1: Overview of creating static TLGs

Lesson 1: Introduction & Concepts ВидеоBasic concepts of TLGsВидеоHow to decide on which TLGs are needed?ВидеоStages of TLG developmentВидеоIntroduction to NESTВидеоKey packages for TLG developmentВидеоLesson 1 OverviewВидео

Lesson 2a: Creating static TLGs with NEST packages

Introduction to Lesson 2ВидеоIntroduction to the Tern packageВидеоTern analyze functionsВидеоWhat is rtables?ВидеоConcept of rtables Видео

Lesson 2b. TLG walk through demonstration

Introduction to demonstrationsВидеоDemography tableВидеоDemography table walk-throughВидеоDemography table conclusionВидеоAdverse Event table introductionВидеоAdverse Event walk-throughВидео

Lesson 3: Introduction to TLG Catalog

Introduction to TLG CatalogВидеоAnatomy of TLG CatalogВидеоFeedback to TLG CatalogВидеоTLG Catalog Demo Part 1ВидеоTLG Catalog Demo Part 2ВидеоLesson 3 SummaryВидео

Lesson 4: More on NEST packages & industry collaborative efforts

More on NEST packagesВидеоIndustry collaboration effortsВидео

Module Review

Quiz - Creating Static TLGs using NEST packagesЗадание
07 Interactive Data Displays31 материалов

Lesson 1: Motivation for interactive data displays

Motivation for Interactive Data DisplaysВидео

Lesson 2: Understanding the teal framework

IntroductionВидеоWhat is teal?ВидеоTeal demoВидеоTeal key featuresВидеоHow does teal work?ВидеоDemo modules using teal.gallery ВидеоUsing teal as a data scientistВидеоTeal framework quizЗадание

Lesson 3: Build your first teal app

IntroductionВидеоTeal installation guideВидеоApp development worflowВидеоApp project setupВидеоFirst teal appВидеоFilters in tealВидеоAdvanced filters

Lesson 4: Build a production-level teal app

IntroductionВидеоTeal app development workflowВидеоData review modulesВидеоLoading dataВидеоCode reproducibilityВидеоProcessing input dataВидеоAdding a demographics table module

Module review

Module reviewВидеоTeal universe product mapЧтениеModule assessment quizЗадание
08Conclusion1 материалов

Conclusion

ConclusionВидео
QCing and Exporting ADaMВидео
Lesson Two - Test your knowledgeЗадание
Links to Pharmaverse Github Repos and SitesЧтение
Relative days of an AE from first exposure to study drugВидео
AE DurationsВидео
Lesson 3 : Test your knowledgeЗадание
Lesson 5 : Test your knowledgeЗадание
Variable Label attributesВидео
Controlled-Terminology checksВидео
Final XPT check and conversionВидео
Lesson 6b: Test your knowledgeЗадание
Adverse Event Table conclusionВидео
Response Table IntroductionВидео
Response table - preprocessing the dataВидео
Response table walk-through part 1Видео
Response Table walk-through part 2Видео
Response Table part 3Видео
Response table walk-through part 4Видео
Response Table walk-through conclusionВидео
Lesson 2 Quiz - Creating Static TLGs with NESTЗадание
Lesson 2 conclusionВидео
Видео
Teal basic concepts quizЗадание
Видео
Adding an adverse events table moduleВидео
Adding a KM plot moduleВидео
Build the full appВидео
Teal advanced concepts quizЗадание