psichomics
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see psichomics.
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Bioconductor version: 3.9
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 "3.6") and enter:
if (!require("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")| 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 | 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 | 1.10.2 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5), shiny (>= 1.0.3), shinyBS |
| Imports | AnnotationDbi, AnnotationHub, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14), recount, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods, org.Hs.eg.db |
| System Requirements | |
| URL | 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 |
| 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_1.10.2.tar.gz |
| Windows Binary | psichomics_1.10.2.zip |
| Mac OS X 10.11 (El Capitan) | psichomics_1.10.2.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 |
| Old Source Packages for BioC 3.9 | Source Archive |