To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("psichomics")

In most cases, you don't need to download the package archive at all.

psichomics

 

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: Release (3.5)

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 gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("psichomics")

Documentation

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
Text   LICENSE

Details

biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialSplicing, GUI, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.2.1
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License MIT + file LICENSE
Depends R (>= 3.3), shiny (>= 1.0.0), shinyBS
Imports AnnotationHub, colourpicker, data.table, digest, dplyr, DT (>= 0.2), fastmatch, ggplot2, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, miscTools, plyr, R.utils, shinyjs, stringr, stats, survival, Sushi, tools, utils, XML, methods
LinkingTo
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car
SystemRequirements
Enhances
URL https://github.com/nuno-agostinho/psichomics
BugReports https://github.com/nuno-agostinho/psichomics/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source psichomics_1.2.1.tar.gz
Windows Binary psichomics_1.2.1.zip
Mac OS X 10.11 (El Capitan) psichomics_1.2.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/psichomics/tree/release-3.5
Package Short Url http://bioconductor.org/packages/psichomics/
Package Downloads Report Download Stats

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