phantasus

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see phantasus.

Visual and interactive gene expression analysis

Bioconductor version: 3.8

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 "3.5") and enter:


if (!require("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")

Developing new tools HTML R Script

Using phantasus application HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, DataRepresentation, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Microarray, Normalization, PrincipalComponent, RNASeq, Software, Transcriptomics, Visualization

Version 1.2.1

In Bioconductor since BioC 3.7 (R-3.5) (6 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, svglite, gtable, stats, Matrix, Matrix.utils, pheatmap, scales, ccaPP, grid, grDevices

System Requirements

URL https://genome.ifmo.ru/phantasus https://artyomovlab.wustl.edu/phantasus

Bug Reports https://github.com/ctlab/phantasus/issues

Suggests testthat, BiocStyle, knitr, rmarkdown, data.table

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