psichomics
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see psichomics.
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Bioconductor version: 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>
citation("psichomics")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("psichomics")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
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) (7.5 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 |
| System Requirements | |
| URL | https://github.com/nuno-agostinho/psichomics |
| Bug Reports | https://github.com/nuno-agostinho/psichomics/issues |
See More
| Suggests | testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/psichomics |
| Package Short Url | https://bioconductor.org/packages/psichomics/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |