Package: SRAdb 1.67.0

Jack Zhu

SRAdb: A compilation of metadata from NCBI SRA and tools

The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

Authors:Jack Zhu and Sean Davis

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SRAdb.pdf |SRAdb.html✨
SRAdb/json (API)
NEWS

# Install 'SRAdb' in R:

install.packages('SRAdb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zhujack/sradb/issues

On BioConductor:SRAdb-1.67.0(bioc 3.20)SRAdb-1.66.0(bioc 3.19)

bioconductor-package

23 exports 3.43 score 52 dependencies 20 mentions

Last updated 2 months agofrom:3b6247319b

Exports:ascpR ascpSRA colDescriptions entityGraph getFASTQfile getFASTQinfo getSRA getSRAdbFile getSRAfile getSRAinfo IGVclear IGVcollapse IGVgenome IGVgoto IGVload IGVsession IGVsnapshot IGVsocket IGVsort listSRAfile sraConvert sraGraph startIGV

Dependencies:Biobase BiocGenerics bit bit64 bitops blob cachem cli clipr cpp11 crayon curl data.table DBI dplyr fansi fastmap generics GEOquery glue graph hms lifecycle limma magrittr memoise pillar pkgconfig plogr prettyunits progress purrr R.methodsS3 R.oo R.utils R6 RCurl readr rlang RSQLite statmod stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs vroom withr xml2

Using SRAdb to Query the Sequence Read Archive

Rendered fromSRAdb.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2019-12-24
Started: 2013-11-01

Help page	Topics
Query NCBI SRA metadata within R or from a local SQLite database	SRAdb-package SRAdb
Fasp file downloading using the ascp command line program	ascpR
Fasp SRA data file downloading using the ascp command line program	ascpSRA
Get column descriptions of SRAmetadb.sqlite	colDescriptions
Create a new graphNEL object from an input entity matrix or data.frame	entityGraph
Download SRA fastq files from EBI ENA through ftp or fasp	getFASTQfile
Get SRA fastq file information and associated meta data from EBI ENA	getFASTQinfo
Fulltext search SRA meta data using SQLite fts3 module	getSRA
Download and unzip last version of SRAmetadb.sqlite.gz from the server	getSRAdbFile
Download SRA data file through ftp or fasp	getSRAfile
Get SRA data file information from NCBI SRA	getSRAinfo
Clear IGV tracks loaded.	IGVclear
Collapse tracks in the IGV	IGVcollapse
Set the IGV genome.	IGVgenome
Go to a specified region in IGV.	IGVgoto
Load data into IGV via remote port call.	IGVload
Create an IGV session file	IGVsession
Make a file snapshot of the current IGV screen.	IGVsnapshot
Create a Socket Connection to IGV.	IGVsocket
Sort an alignment track by the specified option.	IGVsort
List sra, sra-lite or fastq data file names associated with input SRA accessions	listSRAfile
Cross-reference between GEO data types	sraConvert
Create a new graphNEL object of SRA accessios from SRA full text search	sraGraph
Start IGV from R with different amount maximum memory support	startIGV

Package: SRAdb 1.67.0

SRAdb: A compilation of metadata from NCBI SRA and tools

Using SRAdb to Query the Sequence Read Archive

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