phantasusLite
This is the released version of phantasusLite; for the devel version, see phantasusLite.
Loading and annotation RNA-seq counts matrices
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| 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_1.10.0.tar.gz |
| Windows Binary (x86_64) | phantasusLite_1.10.0.zip |
| macOS Binary (big-sur-x86_64) | phantasusLite_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | phantasusLite_1.10.0.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 |