gdscloud
This is the development version of gdscloud; to use it, please install the devel version of Bioconductor.
Cloud Storage Access for GDS Files
Bioconductor version: Development (3.24)
Provides read-only access to GDS (Genomic Data Structure) files stored on cloud storage services including Amazon S3, Google Cloud Storage (GCS), and Azure Blob Storage, as well as any HTTP/HTTPS URL. It extends the 'gdsfmt' package so that cloud URLs (http://, https://, s3://, gs://, az://) can be opened transparently, without downloading the whole file first. Only the blocks that are actually read are fetched, using HTTP Range requests via libcurl together with an in-memory least-recently-used block cache, so that random access to a remote GDS file behaves like access to a local one. Credentials are resolved from the usual environment variables of each service, or set per session and per URL prefix, and they can be exported to the workers of a parallel cluster.
Author: Xiuwen Zheng [aut, cre]
Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>
citation("gdscloud")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("gdscloud")
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("gdscloud")| Cloud Storage Access for GDS Files | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | LGPL-3 |
| Depends | R (>= 4.5.0), gdsfmt(>= 1.49.7) |
| Imports | |
| System Requirements | libcurl (>= 7.28.0), OpenSSL |
| URL | https://github.com/zhengxwen/gdscloud |
| Bug Reports | https://github.com/zhengxwen/gdscloud/issues |
See More
| Suggests | BiocParallel, BiocStyle, keyring, knitr, rmarkdown, testthat, SeqArray |
| Linking To | gdsfmt |
| 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 | gdscloud_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | gdscloud_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/gdscloud |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gdscloud |
| Bioc Package Browser | https://code.bioconductor.org/browse/gdscloud/ |
| Package Short Url | https://bioconductor.org/packages/gdscloud/ |
| Package Downloads Report | Download Stats |