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.
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classificationvisualization
9.13 score 17 stars 1 dependents 276 scripts 1.3k downloadscompcodeR - 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.
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immunooncologyrnaseqdifferentialexpression
8.13 score 12 stars 35 scripts 695 downloadsExploreModelMatrix - 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.
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experimentaldesignregressiondifferentialexpressionshinyapps
8.10 score 38 stars 103 scripts 604 downloadscountsimQC - 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.
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microbiomernaseqsinglecellexperimentaldesignqualitycontrolreportwritingvisualizationimmunooncology
7.79 score 31 stars 42 scripts 1.0k downloadsbettr - 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.
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visualizationshinyappsgui
6.50 score 7 stars 19 scripts 298 downloadstreeclimbR - 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.
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statisticalmethodcellbasedassays
6.40 score 21 stars 60 scripts 304 downloadsalevinQC - 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.
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qualitycontrolsinglecellcpp
6.27 score 31 stars 524 downloadsTabulaMurisSenisData - Bulk and single-cell RNA-seq data from the Tabula Muris Senis project
This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.
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singlecelldataexperimentdatarnaseqdataexperimenthubdatapkg
6.13 score 4 stars 45 scriptsRhisat2 - 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.
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alignmentsequencingsplicedalignmentcpp
5.91 score 3 stars 1 dependents 12 scripts 573 downloadsmutscan - Preprocessing and Analysis of Deep Mutational Scanning Data
Provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.
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geneticvariabilitygenomicvariationpreprocessingzlibcppopenmp
5.89 score 14 stars 14 scripts 280 downloadssketchR - 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.
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singlecell
5.38 score 3 stars 9 scripts 326 downloadsTabulaMurisData - 10x And SmartSeq2 Data From The Tabula Muris Consortium
Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/).
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singlecelldataexperimentdatarnaseqdatadatapkg
4.54 score 23 scriptsdreval - Evaluate Reduced Dimension Representations
Evaluate and compare multiple reduced dimension representations, based on how well they retain structure from the original data set.
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dimensionreductionprincipalcomponentvisualization
3.85 score 7 stars 2 scriptsConfoundingExplorer - 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.
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regressionexperimentaldesignmultiplecomparisonbatcheffect
2.00 score 2 stars 4 scripts