A compilation of metadata from NCBI SRA and tools


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Documentation for package ‘SRAdb’ version 1.8.0

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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
getSRA Fulltext search SRA meta data using SQLite fts3 module
getSRAdbFile Download and unzip last version of SRAmetadb.sqlite.gz from the server
getSRAfile Download sra or sra-lite data files associated with input SRA accessions from NCBI SRA ftp site
getSRAinfo Get file size and date from NCBI ftp site for available sra or sra-lite data files associated with input SRA accessions
IGVclear Clear IGV tracks loaded.
IGVcollapse Collapse tracks in the IGV
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.
IGVsocket Create a Socket Connection to IGV.
IGVsort Sort an alignment track by the specified option.
listSRAfile List sra/sra-lite data 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