psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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.

Package details

AuthorNuno Saraiva-Agostinho [aut, cre] (<>), Nuno Luís Barbosa-Morais [aut, led, ths] (<>), André Falcão [ths], Lina Gallego Paez [ctb], Marie Bordone [ctb], Teresa Maia [ctb], Mariana Ferreira [ctb], Ana Carolina Leote [ctb], Bernardo de Almeida [ctb]
Bioconductor views AlternativeSplicing BiomedicalInformatics DifferentialExpression DifferentialSplicing GUI GeneExpression ImmunoOncology MultipleComparison PrincipalComponent RNASeq Sequencing Survival Transcription Transcriptomics Visualization
MaintainerNuno Saraiva-Agostinho <>
LicenseMIT + file LICENSE
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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psichomics documentation built on Nov. 8, 2020, 5:44 p.m.