<![CDATA[SRA]]>https://www.ncbi.nlm.nih.gov/sra/docs/sra-bigquery-examples/ SRA bigquery

]]>http://an.forum.genostack.com/topic/507/sraRSS for NodeSat, 13 Jun 2026 10:43:59 GMTFri, 31 Dec 2021 15:13:04 GMT60<![CDATA[Reply to SRA on Thu, 27 Jan 2022 06:30:10 GMT]]>https://metasra.biostat.wisc.edu/?species=human&assay=RNA-seq
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https://academic.oup.com/bioinformatics/article/33/18/2914/3848915?login=false

]]>http://an.forum.genostack.com/post/1152http://an.forum.genostack.com/post/1152Thu, 27 Jan 2022 06:30:10 GMT<![CDATA[Reply to SRA on Thu, 27 Jan 2022 05:39:28 GMT]]>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077910

整合SRA GEO Pubmed
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]]>http://an.forum.genostack.com/post/1150http://an.forum.genostack.com/post/1150Thu, 27 Jan 2022 05:39:28 GMT<![CDATA[Reply to SRA on Thu, 27 Jan 2022 05:22:19 GMT]]>https://academic.oup.com/nar/article/48/D1/D776/5626530?login=false
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Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database

]]>http://an.forum.genostack.com/post/1148http://an.forum.genostack.com/post/1148Thu, 27 Jan 2022 05:22:19 GMT<![CDATA[Reply to SRA on Thu, 27 Jan 2022 02:33:01 GMT]]>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

]]>http://an.forum.genostack.com/post/1146http://an.forum.genostack.com/post/1146Thu, 27 Jan 2022 02:33:01 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 12:20:30 GMT]]>https://github.com/louiejtaylor/grabseqs
https://github.com/jfear/sramongo

]]>http://an.forum.genostack.com/post/1144http://an.forum.genostack.com/post/1144Wed, 26 Jan 2022 12:20:30 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 11:33:56 GMT]]>https://github.com/inutano/sra_metadata_toolkit

]]>http://an.forum.genostack.com/post/1143http://an.forum.genostack.com/post/1143Wed, 26 Jan 2022 11:33:56 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 11:33:05 GMT]]>https://github.com/NCBI-Hackathons/MetadataTable

]]>http://an.forum.genostack.com/post/1142http://an.forum.genostack.com/post/1142Wed, 26 Jan 2022 11:33:05 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 10:54:00 GMT]]>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

]]>http://an.forum.genostack.com/post/1140http://an.forum.genostack.com/post/1140Wed, 26 Jan 2022 10:54:00 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 10:49:53 GMT]]>https://github.com/linsalrob/SRA_Metadata

SRA metadata的解析 将xml转换为JSON

]]>http://an.forum.genostack.com/post/1139http://an.forum.genostack.com/post/1139Wed, 26 Jan 2022 10:49:53 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 10:32:02 GMT]]>metadata 表的字段
https://edwards.flinders.edu.au/sra-attributes/

]]>http://an.forum.genostack.com/post/1137http://an.forum.genostack.com/post/1137Wed, 26 Jan 2022 10:32:02 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 10:36:48 GMT]]>https://linsalrob.github.io/ComputationalGenomicsManual/Databases/SRA.html
SRA的基本概念
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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
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GEO和SRA的联动
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]]>http://an.forum.genostack.com/post/1136http://an.forum.genostack.com/post/1136Wed, 26 Jan 2022 10:36:48 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 10:17:36 GMT]]>https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/
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SRA的数据趋势：
https://www.ncbi.nlm.nih.gov/sra/docs/sragrowth/
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]]>http://an.forum.genostack.com/post/1135http://an.forum.genostack.com/post/1135Wed, 26 Jan 2022 10:17:36 GMT<![CDATA[Reply to SRA on Fri, 31 Dec 2021 15:25:56 GMT]]>pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

]]>http://an.forum.genostack.com/post/1049http://an.forum.genostack.com/post/1049Fri, 31 Dec 2021 15:25:56 GMT<![CDATA[Reply to SRA on Fri, 31 Dec 2021 15:21:37 GMT]]>https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-19
SRAdb: query and use public next-generation sequencing data from within R

]]>http://an.forum.genostack.com/post/1048http://an.forum.genostack.com/post/1048Fri, 31 Dec 2021 15:21:37 GMT<![CDATA[Reply to SRA on Wed, 26 Jan 2022 10:59:41 GMT]]>https://www.bioconductor.org/packages/devel/bioc/vignettes/SRAdb/inst/doc/SRAdb.pdf
SRAdb

https://github.com/seandavi/SRAdb
https://www.researchgate.net/publication/275970472_Investigation_into_the_annotation_of_protocol_sequencing_steps_in_the_Sequence_Read_Archive
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https://github.com/saketkc/pysradb

]]>http://an.forum.genostack.com/post/1047http://an.forum.genostack.com/post/1047Wed, 26 Jan 2022 10:59:41 GMT<![CDATA[Reply to SRA on Fri, 31 Dec 2021 15:14:59 GMT]]>https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud-based-examples/

]]>http://an.forum.genostack.com/post/1046http://an.forum.genostack.com/post/1046Fri, 31 Dec 2021 15:14:59 GMT