srametadata
is an R package for getting metadata from Sequence Read Archive (SRA) and making traits prediction.
devtools::install_github("SiruoWang/srametadata")
Package can be loaded into R as follows:
library('srametadata')
Example: Get fastq urls from SRA.
library('srametadata') # Get sqlite database download_sra_db() # Get path to sqlite database sqlfile <- file.path('.', 'SRAmetadb.sqlite') # Create connection conn <- dbConnect(SQLite(),sqlfile) # one file, two files and three files associated with corresponding run accessions get_fastq_urls(runacc = c("DRR001482", "DRR001627", "ERR204978"), db_con = conn)
Example: predict sex from SRA using run accessions.
predictsex(run_accession = "SRR1296065") predictsex(run_accession = c("SRR1296065","SRR1044429"))
Example: normalize gene expression from SRA.
normalized(file = scan("sra_samples.txt", what="", sep="\n"), path = path, chr = "chrY", start = 14813160, end = 14972768)
For questions regarding srametadata
, contact the authors, Jose Alquicira Hernandez and Siruo Wang at
sara.siruo@gmail.com.
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