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 (3.12)

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 <nunodanielagostinho at>, Nuno Barbosa-Morais <nunodanielagostinho at>, Luís Falcão <nunodanielagostinho at>, André Gallego Paez <nunodanielagostinho at>, Lina Bordone <nunodanielagostinho at>, Marie Maia <nunodanielagostinho at>, Teresa Ferreira <nunodanielagostinho at>, Mariana Leote <nunodanielagostinho at>, Ana Carolina de Almeida <nunodanielagostinho at>, Bernardo Saraiva-Agostinho <nunodanielagostinho at>

Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho at>

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


To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel


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


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biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, ImmunoOncology, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.15.0
In Bioconductor since BioC 3.4 (R-3.3) (3.5 years)
License MIT + file LICENSE
Depends R (>= 3.6), shiny (>= 1.0.3), 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, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14), recount, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods,
LinkingTo Rcpp
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling
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