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bslibdash - 'Bootstrap' 5 Dashboard Framework for 'shiny' Apps

Provides a dashboard layer for 'shiny' applications built on 'bslib' and 'Bootstrap' 5. Includes a dashboard page shell, sidebar navigation, cards, value boxes, header drop-down menus and feedback components that inherit the active 'bslib' theme and follow 'Bootstrap' design patterns. Function names mirror those of the 'shinydashboard' package wherever the underlying concepts are shared, allowing existing applications to migrate with minimal changes.

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4.78 score 1 stars 95 downloads

xgxr - Exploratory Graphics for Pharmacometrics

Supports a structured approach for exploring PKPD data <https://opensource.nibr.com/xgx/>. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.

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8.27 score 16 stars 6 dependents 117 scripts 2.2k downloads

OncoBayes2 - Bayesian Logistic Regression for Oncology Dose-Escalation Trials

Bayesian logistic regression model with optional EXchangeability-NonEXchangeability parameter modelling for flexible borrowing from historical or concurrent data-sources. The safety model can guide dose-escalation decisions for adaptive oncology Phase I dose-escalation trials which involve an arbitrary number of drugs. Please refer to Neuenschwander et al. (2008) <doi:10.1002/sim.3230> and Neuenschwander et al. (2016) <doi:10.1080/19466315.2016.1174149> for details on the methodology.

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onetbbcpp

5.68 score 4 stars 40 scripts 571 downloads

monitOS - Monitoring Overall Survival in Pivotal Trials in Indolent Cancers

These guidelines are meant to provide a pragmatic, yet rigorous, help to drug developers and decision makers, since they are shaped by three fundamental ingredients: the clinically determined margin of detriment on OS that is unacceptably high (delta null); the benefit on OS that is plausible given the mechanism of action of the novel intervention (delta alt); and the quantity of information (i.e. survival events) it is feasible to accrue given the clinical and drug development setting. The proposed guidelines facilitate transparent discussions between stakeholders focusing on the risks of erroneous decisions and what might be an acceptable trade-off between power and the false positive error rate.

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indolentmonitoringsurvival

5.38 score 2 stars 2 scripts 204 downloads

synadam - Generate Synthetic ADaM Datasets

Generates synthetic ADaM (Analysis Data Model) datasets from real clinical trial data. Preserves the structure of real datasets (column names, value ranges, relationships between treatment and flag columns) while removing identifiable patient information. Supports subject-level (ADSL), longitudinal (BDS), occurrence (OCCDS), and time-to-event (TTE) dataset types.

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4.70 score 2 stars 245 downloads

peakCombiner - The R package to curate and merge enriched genomic regions into consensus peak sets

peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

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workflowsteppreprocessingchiponchip

3.73 score 6 stars 1 scripts 258 downloads