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psichomics
This is thereleased version of psichomics; for the devel version, seepsichomics.
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Bioconductor version: Release (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: 0000-0002-5549-105X, Nuno Luís Barbosa-Morais [aut, led, ths] 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("psichomics")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("psichomics")For older versions of R, please refer to the appropriateBioconductor 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 | 1.36.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 years) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | psichomics_1.36.0.tar.gz |
| Windows Binary (x86_64) | psichomics_1.36.0.zip |
| macOS Binary (x86_64) | psichomics_1.36.0.tgz |
| macOS Binary (arm64) | psichomics_1.36.0.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 |