<![CDATA[GEO 数据库]]>https://www.mathworks.com/help/bioinfo/ug/working-with-geo-series-data.html

]]>http://an.forum.genostack.com/topic/506/geo-数据库RSS for NodeSat, 13 Jun 2026 09:22:33 GMTFri, 31 Dec 2021 13:59:19 GMT60<![CDATA[Reply to GEO 数据库 on Fri, 28 Jan 2022 02:46:36 GMT]]>https://imageo.genyo.es/#
对GEO进行meta-analysis分析
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]]>http://an.forum.genostack.com/post/1155http://an.forum.genostack.com/post/1155Fri, 28 Jan 2022 02:46:36 GMT<![CDATA[Reply to GEO 数据库 on Sat, 22 Jan 2022 18:10:34 GMT]]>https://hepseq.org/a-content-based-dataset-recommendation-system-for-researchers-a-case-study-on-gene-expression-omnibus-geo-repository/

]]>http://an.forum.genostack.com/post/1127http://an.forum.genostack.com/post/1127Sat, 22 Jan 2022 18:10:34 GMT<![CDATA[Reply to GEO 数据库 on Fri, 07 Jan 2022 16:54:52 GMT]]>一些可以用的git库

https://github.com/guma44/GEOparse
python实现 对标geoquery

https://github.com/jasdumas/shinyGEO

]]>http://an.forum.genostack.com/post/1067http://an.forum.genostack.com/post/1067Fri, 07 Jan 2022 16:54:52 GMT<![CDATA[Reply to GEO 数据库 on Fri, 07 Jan 2022 14:59:56 GMT]]>https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC3531084/

GEO的描述论文
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]]>http://an.forum.genostack.com/post/1066http://an.forum.genostack.com/post/1066Fri, 07 Jan 2022 14:59:56 GMT<![CDATA[Reply to GEO 数据库 on Fri, 07 Jan 2022 15:56:15 GMT]]>https://link.springer.com/article/10.1007/s12551-018-0490-8
Mining data and metadata from the gene expression omnibus
对GEO数据的挖掘做了详细分析
里面提到了一些二次挖掘的工具列表
https://link.springer.com/article/10.1007/s12551-018-0490-8/tables/1
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metadata的三种提炼思路：
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]]>http://an.forum.genostack.com/post/1061http://an.forum.genostack.com/post/1061Fri, 07 Jan 2022 15:56:15 GMT<![CDATA[Reply to GEO 数据库 on Fri, 07 Jan 2022 16:25:35 GMT]]>https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC6333964/
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis
http://www.regeo.org
对GEO做了文本挖掘增加了时间线和疾病功能
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]]>http://an.forum.genostack.com/post/1060http://an.forum.genostack.com/post/1060Fri, 07 Jan 2022 16:25:35 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 16:03:07 GMT]]>https://medicalgenomics.org/rna_seq_atlas

]]>http://an.forum.genostack.com/post/1057http://an.forum.genostack.com/post/1057Fri, 31 Dec 2021 16:03:07 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 16:01:10 GMT]]>https://academic.oup.com/bioinformatics/article/28/8/1184/194911
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing

]]>http://an.forum.genostack.com/post/1056http://an.forum.genostack.com/post/1056Fri, 31 Dec 2021 16:01:10 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 15:59:24 GMT]]>https://www.nature.com/articles/sdata2017125
Precision annotation of digital samples in NCBI’s gene expression omnibus
http://stargeo.org/ 对GEO的所有样本做了标签化注释

]]>http://an.forum.genostack.com/post/1055http://an.forum.genostack.com/post/1055Fri, 31 Dec 2021 15:59:24 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 15:48:49 GMT]]>https://biopython.org/docs/1.75/api/Bio.Geo.html

]]>http://an.forum.genostack.com/post/1053http://an.forum.genostack.com/post/1053Fri, 31 Dec 2021 15:48:49 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 15:45:21 GMT]]>GEORAC: an RNA-seq Atlas Constructor for the
Gene Expression Omnibus
https://dc.uwm.edu/cgi/viewcontent.cgi?article=2880&context=etd

]]>http://an.forum.genostack.com/post/1052http://an.forum.genostack.com/post/1052Fri, 31 Dec 2021 15:45:21 GMT<![CDATA[Reply to GEO 数据库 on Fri, 07 Jan 2022 16:32:06 GMT]]>https://github.com/zhujack/GEOmetadb/
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]]>http://an.forum.genostack.com/post/1051http://an.forum.genostack.com/post/1051Fri, 07 Jan 2022 16:32:06 GMT<![CDATA[Reply to GEO 数据库 on Fri, 07 Jan 2022 08:30:46 GMT]]>https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2308-x
BART: bioinformatics array research tool

]]>http://an.forum.genostack.com/post/1050http://an.forum.genostack.com/post/1050Fri, 07 Jan 2022 08:30:46 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 15:10:41 GMT]]>https://www.researchgate.net/publication/275970472_Investigation_into_the_annotation_of_protocol_sequencing_steps_in_the_Sequence_Read_Archive
SRA的表设计

]]>http://an.forum.genostack.com/post/1044http://an.forum.genostack.com/post/1044Fri, 31 Dec 2021 15:10:41 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 15:03:19 GMT]]>https://ncbiinsights.ncbi.nlm.nih.gov/2021/10/21/geo-sra-dbgap-tracks-genome-data-viewer/
View GEO, SRA, or dbGaP data tracks in NCBI’s Genome Data Viewer

]]>http://an.forum.genostack.com/post/1043http://an.forum.genostack.com/post/1043Fri, 31 Dec 2021 15:03:19 GMT<![CDATA[Reply to GEO 数据库 on Wed, 26 Jan 2022 09:01:29 GMT]]>https://www.nature.com/articles/s41598-019-43935-8
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data

https://github.com/uc-bd2k/GREP2
GEO RNA-seq Experiments Processing Pipeline 一个R实现的pipeline 处理了geo的数据

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]]>http://an.forum.genostack.com/post/1042http://an.forum.genostack.com/post/1042Wed, 26 Jan 2022 09:01:29 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 14:56:49 GMT]]>https://www.qlucore.com/import-and-analyze-public-data-from-sra-geo-and-tcga
Import and analyze public data from SRA, GEO and TCGA

]]>http://an.forum.genostack.com/post/1041http://an.forum.genostack.com/post/1041Fri, 31 Dec 2021 14:56:49 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 14:55:26 GMT]]>https://hbctraining.github.io/Accessing_public_genomic_data/lessons/downloading_from_SRA.html

]]>http://an.forum.genostack.com/post/1040http://an.forum.genostack.com/post/1040Fri, 31 Dec 2021 14:55:26 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 14:46:35 GMT]]>https://github.com/s-andrews/sradownloader
A script to make downloading of SRA/GEO data easier

]]>http://an.forum.genostack.com/post/1039http://an.forum.genostack.com/post/1039Fri, 31 Dec 2021 14:46:35 GMT<![CDATA[Reply to GEO 数据库 on Fri, 31 Dec 2021 14:43:39 GMT]]>Does GEO store raw data?
Yes. GEO requires raw data, processed data and metadata. Raw data facilitates the unambiguous interpretation of the data and potential verification of conclusions. For microarray data, raw data may be supplied either within the Sample record data tables or as external supplementary data files, e.g., Affymetrix CEL. For high-throughput sequencing, GEO brokers the complete set of raw data files, e.g., FASTQ, to the SRA database on your behalf.

GEO如果存的是NGS数据 那么原始数据在SRA上
如何关联GEO和SRA？
https://www.researchgate.net/figure/The-GEO-and-SRA-simple-search-interface-and-search-results-A-The-Simple-Search_fig1_337316408

http://homer.ucsd.edu/homer/basicTutorial/retrieveFiles.html

]]>http://an.forum.genostack.com/post/1038http://an.forum.genostack.com/post/1038Fri, 31 Dec 2021 14:43:39 GMT