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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
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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 |
| 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.
| Source Package | 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 |
| Source Repository | git clone https://git.bioconductor.org/packages/psichomics |
| Package Short Url | http://bioconductor.org/packages/psichomics/ |
| Package Downloads Report | Download Stats |
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