GNOSIS

Genomics explorer using statistical and survival analysis in R

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("GNOSIS")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GUI, ShinyApps, Software, Survival
Version	1.2.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
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
System Requirements
URL	https://github.com/Lydia-King/GNOSIS/
Bug Reports	https://github.com/Lydia-King/GNOSIS/issues

Suggests	BiocStyle, knitr, rmarkdown
Linking To
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	GNOSIS_1.2.0.tar.gz
Windows Binary (x86_64)	GNOSIS_1.2.0.zip
macOS Binary (x86_64)	GNOSIS_1.2.0.tgz
macOS Binary (arm64)	GNOSIS_1.2.0.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