DOI: 10.18129/B9.bioc.psichomics    

This is the development version of psichomics; for the stable release version, see psichomics.

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: Development (3.7)

Interactive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA and GTEx samples.

Author: Nuno Saraiva-Agostinho [aut, cre], Nuno 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 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 Command-line interface tutorial
HTML R Script Custom alternative splicing annotation
HTML R Script Visual interface tutorial
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialSplicing, GUI, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.5.0
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, R.utils, shinyjs, stringr, stats, survival, tools, utils, XML, xtable, methods
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car
Depends On Me
Imports Me
Suggests Me
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