Skip to contents

Installation

You can install the development version of rena from GitHub with:

# install.packages("devtools")
devtools::install_github("natesheehan/rena")
#> Downloading GitHub repo natesheehan/rena@HEAD
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#>          checking for file 'C:\Users\ns651\AppData\Local\Temp\RtmpS0enCm\remotes54ec2e4e2514\natesheehan-rena-8b8bf33/DESCRIPTION' ...  ✔  checking for file 'C:\Users\ns651\AppData\Local\Temp\RtmpS0enCm\remotes54ec2e4e2514\natesheehan-rena-8b8bf33/DESCRIPTION'
#>       ─  preparing 'rena': (517ms)
#>    checking DESCRIPTION meta-information ...  ✔  checking DESCRIPTION meta-information
#>       ─  checking for LF line-endings in source and make files and shell scripts
#>       ─  checking for empty or unneeded directories
#>      Omitted 'LazyData' from DESCRIPTION
#>       ─  building 'rena_0.1.0.tar.gz'
#>      
#> 
#> Installing package into 'C:/Users/ns651/AppData/Local/Temp/RtmpWCakON/temp_libpath8e08357194f'
#> (as 'lib' is unspecified)

Ena File Downloader

The rena package provides tools for bulk downloading read/analysis files from ENA via FTP using the ena-ftp-downloader. download data from the European Nucleotide Archive (ENA).

The function supports two types of downloads:

  • Query-based download: Provide a query string to retrieve specific data.
  • Accession-based download: Provide accession numbers to download specific data.

Installation

You can install the released version of abstr from CRAN with:

Install the development version from GitHub as follows:

remotes::install_github("natesheehan/rena")
#> Skipping install of 'rena' from a github remote, the SHA1 (8b8bf33d) has not changed since last install.
#>   Use `force = TRUE` to force installation
library(rena)

Usage

Arguments

  • download_type: A character specifying the type of download. Use ‘q’ for query-based download or ‘a’ for accession-based download.
  • query: A character string containing the query to retrieve specific data. This is required when using the ‘q’ download type.
  • accession: A character string containing accession numbers. This is required when using the ‘a’ download type.
  • format: A character string specifying the format of the data to download. Valid options are ‘READS_FASTQ’, ‘READS_SUBMITTED’, ‘ANALYSIS_SUBMITTED’, and ‘ANALYSIS_GENERATED’.
  • location: A character string specifying the download location. By default, it uses the current working directory.
  • email: A character string specifying the email address for notifications. By default, no email is sent.

Download data using accessions ids 

rena::ena_download("a", accession = "SAMEA3231268,SAMEA3231287", format = "READS_FASTQ", location = "C:/Users/ns651/OneDrive")

Download data using query 

rena::ena_download("q", query = "result=read_run&query=country=%22Japan%22AND%20depth=168", format = "READS_FASTQ",location = "C:/Users/ns651/OneDrive")

Issues

For support/issues, please contact us at https://www.ebi.ac.uk/ena/browser/support or drop an issue on the github.

Privacy Notice

The execution of this tool may require limited processing of your personal data to function. By using this tool you are agreeing to this as outlined in our Privacy Notice: https://www.ebi.ac.uk/data-protection/privacy-notice/ena-presentation and Terms of Use: https://www.ebi.ac.uk/about/terms-of-use.