phantasus

DOI: 10.18129/B9.bioc.phantasus    

This is the development version of phantasus; for the stable release version, see phantasus.

Visual and interactive gene expression analysis

Bioconductor version: Development (3.9)

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 Artyomov [aut], Alexey Sergushichev [aut, cre]

Maintainer: Alexey Sergushichev <alsergbox at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("phantasus", version = "3.9")

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 Developing new tools
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 1.3.4
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, Matrix.utils, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi
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_1.3.4.tar.gz
Windows Binary phantasus_1.3.4.zip
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/phantasus/
Package Downloads Report Download Stats

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