A compilation of metadata from NCBI SRA and tools

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Documentation for package ‘SRAdb’ version 1.71.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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