The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.
|Author||Jack Zhu and Sean Davis|
|Date of publication||None|
|Maintainer||Jack Zhu <email@example.com>|
ascpR: Fasp file downloading using the ascp command line program
ascpSRA: Fasp SRA data file downloading using the ascp command line...
colDescriptions: Get column descriptions of SRAmetadb.sqlite
entityGraph: Create a new graphNEL object from an input entity matrix or...
getFASTQfile: Download SRA fastq files from EBI ENA through ftp or fasp
getFASTQinfo: Get SRA fastq file information and associated meta data from...
getSRA: Fulltext search SRA meta data using SQLite fts3 module
getSRAdbFile: Download and unzip last version of SRAmetadb.sqlite.gz from...
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...
sraConvert: Cross-reference between GEO data types
SRAdb-package: Query NCBI SRA metadata within R or from a local SQLite...
sraGraph: Create a new graphNEL object of SRA accessios from SRA full...
startIGV: Start IGV from R with different amount maximum memory support