A compilation of metadata from NCBI SRA and tools


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Documentation for package ‘SRAdb’ version 1.2.1

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SRAdb-package Query NCBI SRA metadata within R or from a local SQLite database
colDescriptions Get column descriptions of SRAmetadb.sqlite
entityGraph Create a new graphNEL object from an input entity matrix or data.frame
getFastq Download fastq files associated with input SRA accessions from NCBI SRA ftp site
getFastqInfo Get file size and date from NCBI ftp site for available fastq files associated with input SRA accessions
getSRA Fulltext search SRA meta data using SQLite fts3 module
getSRAdbFile Download and unzip last version of SRAmetadb.sqlite.gz from the server
IGVgenome Set the IGV genome.
IGVgoto Go to a specified region in IGV.
IGVload Load data into IGV via remote port call.
IGVsession Create an IGV session file
IGVsnapshot Make a file snapshot of the current IGV screen.
IGVsnapshotDirectory Set the directory to which IGV will save snapshots.
listFastq List fastq file names associated with input SRA accessions
sraConvert Cross-reference between GEO data types
SRAdb Query NCBI SRA metadata within R or from a local SQLite database
sraGraph Create a new graphNEL object of SRA accessios from SRA full text search
startIGV Start IGV from R with different amount maximum memory support