psichomics

DOI: 10.18129/B9.bioc.psichomics    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see psichomics.

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Bioconductor version: 3.11

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>

Installation

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

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

BiocManager::install("psichomics")

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) tutorial
HTML	R Script	Case study: visual interface
HTML	R Script	Loading SRA, VAST-TOOLS and user-provided RNA-seq data
HTML	R Script	Preparing an Alternative Splicing Annotation for psichomics
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	1.14.4
In Bioconductor since	BioC 3.4 (R-3.3) (4 years)
License	MIT + file LICENSE
Depends	R (>= 4.0), shiny (>= 1.5.0), 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, pairsD3, plyr, Rcpp (>= 0.12.14), recount, Rfast, 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/ 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_1.14.4.tar.gz
Windows Binary	psichomics_1.14.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	psichomics_1.14.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/psichomics
Source Repository (Developer Access)	git clone [email protected]:packages/psichomics
Package Short Url	https://bioconductor.org/packages/psichomics/
Package Downloads Report	Download Stats