SRA
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https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-19
SRAdb: query and use public next-generation sequencing data from within R -
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.
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metadata 表的字段
https://edwards.flinders.edu.au/sra-attributes/ -
https://github.com/linsalrob/SRA_Metadata
SRA metadata的解析 将xml转换为JSON
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https://github.com/seandavi/SRAdbV2
The data served by the SRAdbV2 package are processed in the following steps.Parse SRA XML files into json format (nearly lossless)
Use Apache Spark to transform the data
Load the data from Apache Spark into an ElasticSearch backend
Provide access to the data via a serverless, swagger-based API -
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https://seandavi.github.io/SRAdbV2/
The data served by the SRAdbV2 package are processed in the following steps.Parse SRA XML files into json format (nearly lossless)
Use Apache Spark to transform the data
Load the data from Apache Spark into an ElasticSearch backend
Provide access to the data via a serverless, swagger-based API -
https://academic.oup.com/nar/article/48/D1/D776/5626530?login=false
Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database -
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