GNOSIS

DOI: 10.18129/B9.bioc.GNOSIS  

Genomics explorer using statistical and survival analysis in R

Bioconductor version: Release (3.18)

GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.

Author: Lydia King [aut, cre] , Marcel Ramos [ctb]

Maintainer: Lydia King <l.king18 at universityofgalway.ie>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GNOSIS")

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("GNOSIS")

 

HTML	R Script	GNOSIS Overview
PDF		Reference Manual
Text		NEWS
Text		LICENSE
Video		GNOSIS: an R Shiny app supporting cancer genomics survival analysis with cBioPortal

Details

biocViews	GUI, ShinyApps, Software, Survival
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools
Imports	DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/Lydia-King/GNOSIS/
BugReports	https://github.com/Lydia-King/GNOSIS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GNOSIS_1.0.0.tar.gz
Windows Binary	GNOSIS_1.0.0.zip
macOS Binary (x86_64)	GNOSIS_1.0.0.tgz
macOS Binary (arm64)	GNOSIS_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GNOSIS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GNOSIS
Bioc Package Browser	https://code.bioconductor.org/browse/GNOSIS/
Package Short Url	https://bioconductor.org/packages/GNOSIS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive