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AOE (All Of gene Expression): Index and meta-analysis of gene expression data that works
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00getlistofxRX.pl modified for new DBCLS SRA API Sep 4, 2019
00getlistofxRX.sh Update 00getlistofxRX.sh Dec 15, 2017
00getprojbyid.pl version3 Aug 24, 2018
00getprojsample.pl update for the new API Sep 5, 2019
00getprojsample.sh
00parseprjgse.pl GSE column added Apr 12, 2018
00parseprjgse.sh Bug fixed Apr 12, 2018
01AE2REI.pl updated AOE tab generation script Jul 28, 2017
01xRX2instrument_model.pl instrument_model commented Jul 19, 2018
01xRX2instrument_model.sh Add missing scripts Jan 25, 2019
01xRXjson2AOE.pl Add to generate aetab for AOE Apr 4, 2018
02GEO-AE.pl Add missing scripts Jan 25, 2019
02GEOjson2AOE.pl Add missing scripts Jan 25, 2019
02GEOjson2AOE.sh Add missing scripts Jan 25, 2019
03PRJnotinGEOAE.sh AOE level3 added Apr 12, 2019
03mkAOEtab.pl AOE level3 added Apr 12, 2019
99updateAOEall.sh update for the integration Sep 6, 2019
API_documentation.md Add files via upload Dec 20, 2018
README.md 00getprojbyid.pl added Jul 19, 2018
efetch_GEO.pl Add files via upload Jul 17, 2018
gethoge-and-pigz.cwl Integration of two workflows Dec 13, 2018
perl-gethoge.cwl Integration of two workflows Dec 13, 2018
pigz.cwl Integration of two workflows Dec 13, 2018
xRX2instrument_model.txt.gz xRX(SRA experiment) -> instrument_model relation Jul 28, 2017

README.md

All of gene expression (AOE)

All of gene expression (AOE) has been an index for public transcriptome database.

The version 2 of AOE includes scripts to extract transcriptome sequencing records from Sequence Read Archive (SRA). Data extracted from SRA will be merged with current version of AOE(AOE1). API for SRA data by DBCLS SRA project is fully used to generate the data.

Currently transcriptome data from NCBI GEO is not included in EBI ArrayExpress (since 2017), and we are going to integrate the data from GEO into AOE utilizing DBCLS SRA API.

From ArrayExpress

  • 01AE2REI.pl Generate AOE tab file from ArrayExpress mirror at DDBJ.

Output Example:

ID ProjID AEID Description Date ArrayType ArrayGroup Technology Instrument NGSGroup Organisms Rep_organism
1 NA E-DORD-69 Translation profiling of Arabidopsis cell cultures exposed to elevated temperature and high salinity 2010-07-07 Agilent Arabidopsis 3 Oligo Microarray 4x44K 015059 G2519F (Gene ID version)(A-DORD-1)[24] Agilent array assay NA NA Arabidopsis thaliana[24] Arabidopsis thaliana

From GEO (DBCLS SRA API)

  • 00getprojsample.pl Extract GEO associated SRA/BioProject/BioSample data from DBCLS SRA API.
  • 01GEOjson2AOE.pl Make subset of AOE tab file from extracted json file(s).
  • 00getlistofxRX.pl Get metadata from D/E/SRX (Experiment).

From RNA-seq data not in GEO and ArrayExpress (DBCLS SRA API)

  • 01xRX2instrument_model.pl Extract Instrument_model from SRA Experiment data.
  • 00getprojbyid.pl Fetch BioProject JSON by IDs via DBCLS SRA API.
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