EnhancedVolcano - Publication-ready volcano plots with enhanced colouring and labeling
Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.
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rnaseqgeneexpressiontranscriptiondifferentialexpressionimmunooncology
13.26 score 464 stars 4 dependents 4.0k scripts 10k downloadsPCAtools - PCAtools: Everything Principal Components Analysis
Principal Component Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This 'summary' of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular - users can also identify optimal number of principal components via different metrics, such as elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.
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rnaseqatacseqgeneexpressiontranscriptionsinglecellprincipalcomponentcpp
11.79 score 380 stars 2 dependents 952 scripts 2.0k downloadsVizModules - Flexible, Interactive 'shiny' Modules for Almost Any Plot
Offers a core selection of interactivity-first 'shiny' modules for many plot types meant to serve as flexible building blocks for applications and as the base for more complex modules. These modules allow for the rapid and convenient construction of 'shiny' apps with very few lines of code and decouple plotting from the underlying data. These modules allow for full plot aesthetic customization by the end user through UI inputs. Utility functions for simple UI organization, automated UI tooltips, and additional plot enhancements are also provided. Includes a multi-panel figure builder app for arranging multiple modules together in a free-form layout.
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data-visualizationmodulesshinyvisualization
7.03 score 2 stars 95 scripts 408 downloadsCRISPRball - Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering
A Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.
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softwareshinyappscrisprqualitycontrolvisualizationguicrispr-screendata-visualizationinteractive-visualizationsmageckplotlyscreeningshiny
5.80 score 13 stars 24 scripts 255 downloads