phantasusLite
Loading and annotation RNA-seq counts matrices
Bioconductor version: Release (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("phantasusLite")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, RNASeq, Software, Transcriptomics |
| Version | 1.2.0 |
| 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_1.2.0.tar.gz |
| Windows Binary (x86_64) | phantasusLite_1.2.0.zip |
| macOS Binary (x86_64) | phantasusLite_1.2.0.tgz |
| macOS Binary (arm64) | phantasusLite_1.2.0.tgz |
| 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 |