psichomics

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 gmail.com>

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	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
Text		LICENSE

Details

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
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.

Source Package	psichomics_1.4.5.tar.gz
Windows Binary	psichomics_1.4.5.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	psichomics_1.4.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/psichomics
Package Short Url	http://bioconductor.org/packages/psichomics/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive