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phantasusLite

Loading and annotation RNA-Seq counts matrices


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("phantasusLite")

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("phantasusLite")
phantasusLite tutorial HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews GeneExpression, RNASeq, Software, Transcriptomics
Version 1.0.0
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
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 phantasusLite_1.0.0.tar.gz
Windows Binary phantasusLite_1.0.0.zip
macOS Binary (x86_64) phantasusLite_1.0.0.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