DOI: 10.18129/B9.bioc.psichomics  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see psichomics.

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: 3.16

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")):


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HTML R Script 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
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, ImmunoOncology, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.24.0
In Bioconductor since BioC 3.4 (R-3.3) (6.5 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
LinkingTo Rcpp
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling
Depends On Me
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