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This is the development version of phantasusLite; for the stable release version, see phantasusLite.

Loading and annotation RNA-Seq counts matrices

Bioconductor version: Development (3.19)

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

Author: Rita Sablina [aut], Maxim Kleverov [aut], Alexey Sergushichev [aut, cre]

Maintainer: Alexey Sergushichev <alsergbox at gmail.com>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

phantasusLite tutorial HTML R Script
Reference Manual PDF


biocViews GeneExpression, RNASeq, Software, Transcriptomics
Version 1.1.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3)
Imports data.table, rhdf5client(>= 1.21.5), httr, stringr, stats, utils, Biobase, methods
System Requirements
URL https://github.com/ctlab/phantasusLite/
Bug Reports https://github.com/ctlab/phantasusLite/issues
See More
Suggests testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery
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Package Archives

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

Source Package phantasusLite_1.1.0.tar.gz
Windows Binary phantasusLite_1.1.0.zip
macOS Binary (x86_64) phantasusLite_1.1.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/phantasusLite
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phantasusLite
Bioc Package Browser https://code.bioconductor.org/browse/phantasusLite/
Package Short Url https://bioconductor.org/packages/phantasusLite/
Package Downloads Report Download Stats