Registration Open for Bioc2024 July 24-26


Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: Release (3.19)

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.

Author: Nuno 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]

Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho at>

Citation (from within R, enter citation("psichomics")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Case study: command-line interface (CLI) tutorial HTML R Script
Case study: visual interface tutorial HTML R Script
Loading user-provided data HTML R Script
Preparing an Alternative Splicing Annotation for psichomics HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, ImmunoOncology, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (8 years)
License MIT + file LICENSE
Depends R (>= 4.0), shiny (>= 1.7.0), shinyBS
Imports AnnotationDbi, AnnotationHub, BiocFileCache, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods
System Requirements
Bug Reports
See More
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling
Linking To Rcpp
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package psichomics_1.30.0.tar.gz
Windows Binary
macOS Binary (x86_64) psichomics_1.30.0.tgz
macOS Binary (arm64) psichomics_1.30.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats