GA4GHshiny

This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package.

A tool for unsupervised clustering and analysis of single cell RNA-Seq data.

This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.