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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 (3.22)

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 iD ORCID: 0000-0002-5549-105X , Nuno Luís Barbosa-Morais [aut, led, ths] ORCID iD ORCID: 0000-0002-1215-0538 , 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

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

browseVignettes("psichomics")
Case study: command-line interface (CLI) tutorial HTML R Script
Case study: visual interface tutorial HTML R Script
Loading user-provided data HTML R Script
Preparing an Alternative Splicing Annotation for psichomics HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

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 1.35.0
In Bioconductor since BioC 3.4 (R-3.3) (8.5 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
See More
Suggests testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling
Linking To Rcpp
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Package Archives

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

Source Package psichomics_1.35.0.tar.gz
Windows Binary (x86_64) psichomics_1.35.0.zip
macOS Binary (x86_64) psichomics_1.35.0.tgz
macOS Binary (arm64) psichomics_1.35.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/psichomics
Source Repository (Developer Access) git clone [email protected]:packages/psichomics
Bioc Package Browser https://code.bioconductor.org/browse/psichomics/
Package Short Url https://bioconductor.org/packages/psichomics/
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