phantasus
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see phantasus.
Visual and interactive gene expression analysis
Bioconductor version: 3.19
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>
citation("phantasus")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DataRepresentation, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Microarray, Normalization, PrincipalComponent, RNASeq, Software, Transcriptomics, Visualization |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3) |
| Imports | ggplot2, protolite, Biobase, GEOquery, Rook, 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, 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | phantasus_1.24.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | phantasus_1.24.0.tgz |
| macOS Binary (arm64) | phantasus_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/phantasus |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/phantasus |
| Bioc Package Browser | https://code.bioconductor.org/browse/phantasus/ |
| Package Short Url | https://bioconductor.org/packages/phantasus/ |
| Package Downloads Report | Download Stats |