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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6.71 score 3 stars 3 dependents 96 scripts 417 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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6.26 score 12 stars 34 scripts 269 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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6.23 score 2 stars 40 scripts 387 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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4.85 score 7 stars 8 scripts 606 downloads

a4Preproc - Automated Affymetrix Array Analysis Preprocessing Package

Utility functions to pre-process data for the Automated Affymetrix Array Analysis set of packages.

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microarraypreprocessing

4.46 score 3 dependents 16 scripts 572 downloads

a4Core - Automated Affymetrix Array Analysis Core Package

Utility functions for the Automated Affymetrix Array Analysis set of packages.

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microarrayclassification

4.38 score 4 dependents 7 scripts 595 downloads

a4 - Automated Affymetrix Array Analysis Umbrella Package

Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.

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microarray

3.86 score 36 scripts 564 downloads

a4Reporting - Automated Affymetrix Array Analysis Reporting Package

Utility functions to facilitate the reporting of the Automated Affymetrix Array Analysis Reporting set of packages.

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microarray

3.78 score 1 dependents 3 scripts 500 downloads

a4Classif - Automated Affymetrix Array Analysis Classification Package

Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages.

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microarraygeneexpressionclassification

3.78 score 1 dependents 4 scripts 504 downloads

esetVis - Visualizations of expressionSet Bioconductor object

Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.

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visualizationdatarepresentationdimensionreductionprincipalcomponentpathways

3.34 score 11 scripts 421 downloads

a4Base - Automated Affymetrix Array Analysis Base Package

Base utility functions are available for the Automated Affymetrix Array Analysis set of packages.

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microarray

2.95 score 1 dependents 9 scripts 524 downloads

nlcv - Nested Loop Cross Validation

Nested loop cross validation for classification purposes for misclassification error rate estimation. The package supports several methodologies for feature selection: random forest, Student t-test, limma, and provides an interface to the following classification methods in the 'MLInterfaces' package: linear, quadratic discriminant analyses, random forest, bagging, prediction analysis for microarray, generalized linear model, support vector machine (svm and ksvm). Visualizations to assess the quality of the classifier are included: plot of the ranks of the features, scores plot for a specific classification algorithm and number of features, misclassification rate for the different number of features and classification algorithms tested and ROC plot. For further details about the methodology, please check: Markus Ruschhaupt, Wolfgang Huber, Annemarie Poustka, and Ulrich Mansmann (2004) <doi:10.2202/1544-6115.1078>.

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2.00 score 8 scripts 584 downloads