DOI: 10.18129/B9.bioc.psichomics    

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: Release (3.6)

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression from large transcriptomic datasets, including those from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression project (GTEx), as well as user-owned 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 and enter:

## try http:// if https:// URLs are not supported


HTML R Script Case study: command-line interface (CLI)
HTML R Script Case study: visual interface
HTML R Script Custom alternative splicing annotation
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.4.5
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
License MIT + file LICENSE
Depends R (>= 3.4), shiny (>= 1.0.3), shinyBS
Imports AnnotationHub, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14), R.utils, shinyjs, stringr, stats, survival, tools, utils, XML, xtable, methods
LinkingTo Rcpp
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car
Depends On Me
Imports Me
Suggests Me
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