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uc-bd2k / GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator
https://shiny.ilincs.org/grein
GNU General Public License v2.0
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API for download and TPM calculation #8

Closed OrielResearchCure closed 4 years ago

OrielResearchCure commented 4 years ago

Hello,

The GREIN looks great! I am interested in downloading expression files for blood samples from GEO. What will be the best way to do so? also, please let me know if I have transcripts counts and the genome reference version to transfer the measurements to TPM

Many thanks, Eila

naimmahi commented 4 years ago

Hi Eila,

Unfortunately bulk data download is not available in GREIN. Individual datasets can be downloaded one-by-one. You have to search for blood sample specific datasets (by GEO id) or search by keyword either in the ontology search box or in the data table search box. GREIN provides download options for both transcript level data (TPM) and gene level data (CPM). You have to choose the option in the "Counts table" tab. Hope that helps.

Thanks, Naim