phantasus

DOI: 10.18129/B9.bioc.phantasus    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see phantasus.

Visual and interactive gene expression analysis

Bioconductor version: 3.12

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

Author: Daria Zenkova [aut], Vladislav Kamenev [aut], Rita Sablina [ctb], Maxim Kleverov [ctb], Maxim Artyomov [aut], Alexey Sergushichev [aut, cre]

Maintainer: Alexey Sergushichev <alsergbox at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("phantasus")

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("phantasus")

 

HTML	R Script	Using phantasus application
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, DataRepresentation, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Microarray, Normalization, PrincipalComponent, RNASeq, Software, Transcriptomics, Visualization
Version	1.10.0
In Bioconductor since	BioC 3.7 (R-3.5) (3 years)
License	MIT + file LICENSE
Depends	R (>= 3.5)
Imports	ggplot2, protolite, Biobase, GEOquery, Rook, htmltools, httpuv, jsonlite, limma, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea(>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, curl
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, data.table
SystemRequirements
Enhances
URL	https://genome.ifmo.ru/phantasus https://artyomovlab.wustl.edu/phantasus
BugReports	https://github.com/ctlab/phantasus/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	phantasus_1.10.0.tar.gz
Windows Binary	phantasus_1.10.0.zip
macOS 10.13 (High Sierra)	phantasus_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phantasus
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/phantasus
Package Short Url	https://bioconductor.org/packages/phantasus/
Package Downloads Report	Download Stats