A compilation of metadata from NCBI SRA and tools

Documentation for package ‘SRAdb’ version 1.6.0

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