Package: phantasus 1.33.1

Alexey Sergushichev

phantasus: Visual and interactive gene expression analysis

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.

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

phantasus_1.33.1.tar.gz
phantasus_1.33.1.zip(r-4.7)phantasus_1.33.1.zip(r-4.6)phantasus_1.33.1.zip(r-4.5)
phantasus_1.33.1.tgz(r-4.6-any)phantasus_1.33.1.tgz(r-4.5-any)
phantasus_1.33.1.tar.gz(r-4.7-any)phantasus_1.33.1.tar.gz(r-4.6-any)
phantasus_1.33.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phantasus/json (API)

# Install 'phantasus' in R:

install.packages('phantasus', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

es - Example dataset
fgseaExample - Example pathway data.frame for fgsea tool

On BioConductor:phantasus-1.33.0(bioc 3.24)phantasus-1.32.0(bioc 3.23)

geneexpression gui visualization datarepresentation transcriptomics rnaseq microarray normalization clustering differentialexpression principalcomponent immunooncology

7.40 score 45 stars 20 scripts 10 exports 153 dependencies

Last updated from:8b6bd62ba6. Checks:4 ERROR, 4 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	268
linux-devel-x86_64	NOTE	489
source / vignettes	OK	346
linux-release-x86_64	NOTE	453
macos-release-arm64	NOTE	311
macos-oldrel-arm64	NOTE	305
windows-devel	ERROR	420
windows-release	ERROR	376
windows-oldrel	ERROR	351
wasm-release	OK	274

Exports:generatePreloadedSession getES getGDS getGSE getPhantasusConf read.gct reparseCachedESs servePhantasus setupPhantasus write.gct

Dependencies:abind AnnotationDbi apeglm askpass assertthat base64enc bbmle bdsmatrix BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel Biostrings bit bit64 blob brew cachem ccaPP cli clipr coda codetools config cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray DEoptimR DESeq2 digest dir.expiry dplyr edgeR emdbook evaluate farver fastmap fastmatch fgsea filelock formatR fs futile.logger futile.options generics GenomicRanges GEOquery ggplot2 glue gtable highr hms htmltools httpuv httr httr2 IRanges isoband jsonlite KEGGREST knitr labeling lambda.r later lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mvtnorm numDeriv opencpu openssl otel pcaPP phantasusLite pheatmap pillar pkgconfig plyr png prettyunits progress promises protolite purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppNumerical readr remotes rentrez rhdf5 rhdf5client rhdf5filters Rhdf5lib rjson rlang robustbase RSQLite rvest S4Arrays S4Vectors S7 scales selectr Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment svglite sys systemfonts textshaping tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom webutils withr xfun XML xml2 XVector yaml zip

Using Phantasus application

Rendered fromphantasus-tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-06-29
Started: 2017-07-26

Help page	Topics
Example dataset	es
Example pathway data.frame for fgsea tool	fgseaExample
Generate files for preloaded session from a session link.	generatePreloadedSession
Load ExpressionSet by GEO identifier	getES
Load ExpressionSet from GEO Datasets	getGDS
Load ExpressionSet from GEO Series	getGSE
Read Phantasus Config	getPhantasusConf
Reads ExpressionSet from a GCT file. Function is deprecated, please use phantasusLite:::readGct() instead	read.gct
Reparse cached expression sets from GEO.	reparseCachedESs
Serve phantasus.	servePhantasus
Setup phantasus. Read user config file ( or create default one) and fill 'cache_root' using sources in 'file'.	setupPhantasus
Saves ExpressionSet to a GCT file (version 1.3). Function is deprecated, please use phantasusLite:::writeGct() instead	write.gct

Package: phantasus 1.33.1

phantasus: Visual and interactive gene expression analysis

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)