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")):Xiuwen Zheng. gdscloud: Cloud Storage Access for GDS Files. doi:10.18129/B9.bioc.gdscloud, R package version 0.99.5, https://bioconductor.org/packages/gdscloud.
Generated from the package metadata; it may differ from the package's own citation.
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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 0.99.5 |
| 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; >= 7.32.0 recommended), 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, httpuv, callr, openssl, withr |
| Linking To | gdsfmt |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gdscloud_0.99.5.tar.gz |
| Windows Binary (x86_64) | gdscloud_0.99.5.zip |
| macOS Binary (big-sur-x86_64) | gdscloud_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | gdscloud_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gdscloud |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gdscloud |
| Package Short Url | https://bioconductor.org/packages/gdscloud/ |
| Package Downloads Report | Download Stats |