phantasus
This is the released version of phantasus; for the devel version, see phantasus.
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("phantasus")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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_1.32.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/phantasus/ |
| Package Short Url | https://bioconductor.org/packages/phantasus/ |
| Package Downloads Report | Download Stats |