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 (3.21)

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] (ORCID: ), Nuno Luís Barbosa-Morais [aut, led, ths] (ORCID: ), 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 "4.5") and enter:


if (!require("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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, ImmunoOncology, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization
Version	1.33.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 years)
License	MIT + file LICENSE
Depends	R (>= 4.0), shiny (>= 1.7.0), 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, purrr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods
System Requirements
URL	https://nuno-agostinho.github.io/psichomics/ https://github.com/nuno-agostinho/psichomics/
Bug Reports	https://github.com/nuno-agostinho/psichomics/issues

Suggests	testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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