psichomics

DOI: 10.18129/B9.bioc.psichomics    

This is the development version of psichomics; for the stable release version, see psichomics.

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: Development (3.12)

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 <nunodanielagostinho at gmail.com>, Nuno Barbosa-Morais <nunodanielagostinho at gmail.com>, Luís Falcão <nunodanielagostinho at gmail.com>, André Gallego Paez <nunodanielagostinho at gmail.com>, Lina Bordone <nunodanielagostinho at gmail.com>, Marie Maia <nunodanielagostinho at gmail.com>, Teresa Ferreira <nunodanielagostinho at gmail.com>, Mariana Leote <nunodanielagostinho at gmail.com>, Ana Carolina de Almeida <nunodanielagostinho at gmail.com>, Bernardo Saraiva-Agostinho <nunodanielagostinho at gmail.com>

Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho at gmail.com>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("psichomics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, ImmunoOncology, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.15.0
In Bioconductor since BioC 3.4 (R-3.3) (3.5 years)
License MIT + file LICENSE
Depends R (>= 3.6), shiny (>= 1.0.3), 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, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14), recount, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods, org.Hs.eg.db
LinkingTo Rcpp
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling
SystemRequirements
Enhances
URL https://nuno-agostinho.github.io/psichomics/
BugReports https://github.com/nuno-agostinho/psichomics/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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/
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