SRA

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pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

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https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/

SRA的数据趋势：
https://www.ncbi.nlm.nih.gov/sra/docs/sragrowth/

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https://linsalrob.github.io/ComputationalGenomicsManual/Databases/SRA.html
SRA的基本概念

SRA 操作手册：
https://www.ncbi.nlm.nih.gov/core/assets/sra/files/Factsheet_SRA.pdf

https://hbctraining.github.io/Accessing_public_genomic_data/lessons/downloading_from_SRA.html

GEO和SRA的联动

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metadata 表的字段
https://edwards.flinders.edu.au/sra-attributes/

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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://github.com/NCBI-Hackathons/MetadataTable

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https://github.com/inutano/sra_metadata_toolkit

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https://github.com/louiejtaylor/grabseqs
https://github.com/jfear/sramongo

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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

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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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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077910

整合SRA GEO Pubmed

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https://metasra.biostat.wisc.edu/?species=human&assay=RNA-seq

https://academic.oup.com/bioinformatics/article/33/18/2914/3848915?login=false