iCOBRA - Comparison and Visualization of Ranking and Assignment Methods

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. Various types of performance plots can be generated programmatically. The package also contains a shiny application for interactive exploration of results.

Last updated 20 days ago

classificationvisualization

8.78 score 14 stars 1 packages 192 scripts 596 downloads

ExploreModelMatrix - Graphical Exploration of Design Matrices

Given a sample data table and a design formula, ExploreModelMatrix generates an interactive application for exploration of the resulting design matrix. This can be helpful for interpreting model coefficients and constructing appropriate contrasts in (generalized) linear models. Static visualizations can also be generated.

Last updated 20 days ago

experimentaldesignregressiondifferentialexpressionshinyapps

8.03 score 36 stars 75 scripts 326 downloads

compcodeR - RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

Last updated 20 days ago

immunooncologyrnaseqdifferentialexpression

7.92 score 10 stars 26 scripts 252 downloads

countsimQC - Compare Characteristic Features of Count Data Sets

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

Last updated 20 days ago

microbiomernaseqsinglecellexperimentaldesignqualitycontrolreportwritingvisualizationimmunooncology

7.59 score 27 stars 24 scripts 454 downloads

treeclimbR - An algorithm to find optimal signal levels in a tree

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

Last updated 24 days ago

statisticalmethodcellbasedassays

7.11 score 19 stars 45 scripts 164 downloads

alevinQC - Generate QC Reports For Alevin Output

Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.

Last updated 20 days ago

qualitycontrolsinglecell

6.77 score 31 stars 21 scripts 354 downloads

Rhisat2 - R Wrapper for HISAT2 Aligner

An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

Last updated 20 days ago

alignmentsequencingsplicedalignment

5.95 score 3 stars 1 packages 6 scripts 474 downloads

bettr - A Better Way To Explore What Is Best

bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations.

Last updated 20 days ago

visualizationshinyappsgui

5.43 score 3 stars 3 scripts 145 downloads

sketchR - An R interface for python subsampling/sketching algorithms

Provides an R interface for various subsampling algorithms implemented in python packages. Currently, interfaces to the geosketch and scSampler python packages are implemented. In addition it also provides diagnostic plots to evaluate the subsampling.

Last updated 24 days ago

singlecell

5.34 score 2 stars 3 scripts 194 downloads

dreval - Evaluate Reduced Dimension Representations

Evaluate and compare multiple reduced dimension representations, based on how well they retain structure from the original data set.

Last updated 4 months ago

dimensionreductionprincipalcomponentvisualization

4.02 score 7 stars 2 scripts

ConfoundingExplorer - Confounding Explorer

This package provides a simple interactive application for investigating the effect of confounding between a signal of interest and a batch effect. It uses simulated data with user-specified effect sizes for both batch and condition effects. The user can also specify the number of samples in each condition and batch, and thereby the degree of confounding.

Last updated 4 months ago

regressionexperimentaldesignmultiplecomparisonbatcheffect

2.48 score 2 stars 3 scripts