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 (3.20)
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("psichomics")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | AlternativeSplicing, BiomedicalInformatics, DifferentialExpression, DifferentialSplicing, GUI, GeneExpression, ImmunoOncology, MultipleComparison, PrincipalComponent, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization |
Version | 1.31.0 |
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 |
See More
Suggests | testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling |
Linking To | Rcpp |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | psichomics_1.31.0.tar.gz |
Windows Binary | psichomics_1.31.0.zip |
macOS Binary (x86_64) | psichomics_1.31.0.tgz |
macOS Binary (arm64) | psichomics_1.31.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/psichomics |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/psichomics |
Bioc Package Browser | https://code.bioconductor.org/browse/psichomics/ |
Package Short Url | https://bioconductor.org/packages/psichomics/ |
Package Downloads Report | Download Stats |