phantasus

This is the released version of phantasus; for the devel version, see phantasus.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Visual and interactive gene expression analysis

Bioconductor version: Release (3.23)

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

Maintainer: Alexey Sergushichev <alsergbox at gmail.com>

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

Maxim Kleverov, Daria Zenkova, Vladislav Kamenev, Maxim Artyomov, Alexey Sergushichev. phantasus: Visual and interactive gene expression analysis. doi:10.18129/B9.bioc.phantasus, R package version 1.32.0, https://bioconductor.org/packages/phantasus.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.3)
Imports	ggplot2, protolite, Biobase, GEOquery, htmltools, httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, data.table, curl, apeglm, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs, phantasusLite, XML
System Requirements
URL	https://alserglab.wustl.edu/phantasus
Bug Reports	https://github.com/ctlab/phantasus/issues

Suggests	testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	phantasus_1.32.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	phantasus_1.32.0.tgz
macOS Binary (sonoma-arm64)	phantasus_1.32.0.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