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editbl - 'DT' Extension for CRUD (Create, Read, Update, Delete) Applications in 'shiny'

The core of this package is a function eDT() which enhances DT::datatable() such that it can be used to interactively modify data in 'shiny'. By the use of generic 'dplyr' methods it supports many types of data storage, with relational databases ('dbplyr') being the main use case.

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7.07 score 31 stars 30 scripts 351 downloads

clinUtils - General Utility Functions for Analysis of Clinical Data

Utility functions to facilitate the import, the reporting and analysis of clinical data. Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate the package functionalities.

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6.75 score 3 stars 3 dependents 104 scripts 394 downloads

clinDataReview - Clinical Data Review Tool

Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.

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6.44 score 12 stars 51 scripts 410 downloads

inTextSummaryTable - Creation of in-Text Summary Table

Creation of tables of summary statistics or counts for clinical data (for 'TLFs'). These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report (Word format) or a 'topline' presentation (PowerPoint format), or as interactive table (with the 'DT' package) to an html document for clinical data review.

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6.21 score 2 stars 58 scripts 371 downloads

BIGL - Biochemically Intuitive Generalized Loewe Model

Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.

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6.17 score 8 stars 46 scripts 396 downloads

patientProfilesVis - Visualization of Patient Profiles

Creation of patient profile visualizations for exploration, diagnostic or monitoring purposes during a clinical trial. These static visualizations display a patient-specific overview of the evolution during the trial time frame of parameters of interest (as laboratory, ECG, vital signs), presence of adverse events, exposure to a treatment; associated with metadata patient information, as demography, concomitant medication. The visualizations can be tailored for specific domain(s) or endpoint(s) of interest. Visualizations are exported into patient profile report(s) or can be embedded in custom report(s).

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5.05 score 8 stars 14 scripts 690 downloads

daVis - Visualization Of Differential Expression Analysis

This package contains utility functions to visualize the output from differential expression analysis. The input can be either a model or a list of top tables or a combination of the two. The model can be output from limma, edgeR or DESeq2.

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visualizationdatarepresentationdifferentialexpressionsoftwaremicroarrayrnaseq

4.40 score 4 scripts

tinytest2JUnit - Convert 'tinytest' Output to JUnit XML

Unit testing is a solid component of automated CI/CD pipelines. 'tinytest' - a lightweight, zero-dependency alternative to 'testthat' was developed. To be able to integrate 'tinytests' results into common CI/CD systems the 'tinytests'-object is converted to JUnit XML format. 'tinytest2JUnit' enables this conversion while staying lightweight, having only 'tinytest' as its dependency.

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4.20 score 4 stars 591 downloads