psichomics
This is the released version of psichomics; for the devel version, see psichomics.
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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) 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 | 1.38.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 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_1.38.1.tar.gz |
| Windows Binary (x86_64) | psichomics_1.38.1.zip |
| macOS Binary (big-sur-x86_64) | psichomics_1.38.1.tgz |
| macOS Binary (sonoma-arm64) | psichomics_1.38.1.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 3.23 | Source Archive |