psichomics

DOI: 10.18129/B9.bioc.psichomics    

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: Release (3.8)

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("psichomics", version = "3.8")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("psichomics")

 

HTML R Script Case study: command-line interface (CLI)
HTML R Script Case study: visual interface
HTML R Script Preparing alternative splicing annotations
HTML R Script SRA and user-provided RNA-seq data analysis
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, ImmunoOncology, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version 1.8.1
In Bioconductor since BioC 3.4 (R-3.3) (2 years)
License MIT + file LICENSE
Depends R (>= 3.5), 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), recount, R.utils, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods
LinkingTo Rcpp
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi
SystemRequirements
Enhances
URL https://github.com/nuno-agostinho/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 psichomics_1.8.1.tar.gz
Windows Binary psichomics_1.8.1.zip
Mac OS X 10.11 (El Capitan) psichomics_1.8.1.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 http://bioconductor.org/packages/psichomics/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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