phantasusLite
This is the development version of phantasusLite; for the stable release version, see phantasusLite.
Loading and annotation RNA-seq counts matrices
Bioconductor version: Development (3.21)
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("phantasusLite")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | GeneExpression, RNASeq, Software, Transcriptomics |
Version | 1.5.0 |
In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
License | MIT + file LICENSE |
Depends | R (>= 4.2) |
Imports | data.table, rhdf5client(>= 1.25.1), 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 | phantasus |
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_1.5.0.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
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 |