A compilation of metadata from NCBI SRA and tools


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Documentation for package ‘SRAdb’ version 1.56.0

Help Pages

SRAdb-package Query NCBI SRA metadata within R or from a local SQLite database
ascpR Fasp file downloading using the ascp command line program
ascpSRA Fasp SRA data file downloading using the ascp command line program
colDescriptions Get column descriptions of SRAmetadb.sqlite
entityGraph Create a new graphNEL object from an input entity matrix or data.frame
getFASTQfile Download SRA fastq files from EBI ENA through ftp or fasp
getFASTQinfo Get SRA fastq file information and associated meta data from EBI ENA
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 data file through ftp or fasp
getSRAinfo Get SRA data file information from NCBI SRA
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 or fastq 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