Is it possible to bulk download files from GEO repository?

I am interested in accessing raw RNASeq data files from published manuscripts that are host in Gene Expression Omnibus. Is it possible to download them in bulk rather one by one?

Also is it possible to upload data to Galaxy directly from GEO?

Thank you for considering my request.

rna-seq galaxy tanscriptomics

• 1,463 views • link

updated 2.3 years ago by noodle

• written 2.3 years ago by WUSCHEL

Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/

• 0 views • link

written 2.3 years ago by GenoMax

2 answers

Try using this library GEOparse

• 0 views • link

written 2.3 years ago by atharvakarkare14 •

Also try the NCBI AWS bucket transfer tool. It's extremely convenient, however it's not instantaneous and you need to have a (paid) AWS account.

• 0 views • link

written 2.3 years ago by noodle

More posts like this

RNA-seq
written 2.1 years ago by candy •

galaxy server doesn't give me accurate result although i have put raw data and meta data obtained from GEO database of plant species to see …
From TPM to raw counts
written 2.7 years ago by Gama313

I am deconvoluting a bulk RNASeq experiment using scRNA to generate a signature of cell types using CIBERSORTX. The program asks you bulk data normalized, …
RNASeq Analysis — Galaxy Australia
written 4.6 years ago by WUSCHEL

I am a biologist do not have very good exposure to bioinformatics. Recently I came across some of my colleagues are using Galaxy Australia to …
Tutorial: RNASeq tutorial for gene differential expression analysis
written 6.0 years ago by Thind amarinder

**RNA-seq-tutorial-for-gene-differential-expression-analysis** This tutorial is based on Bioconductor packages, RNAseq gene differential expression analysis, including filtering, preprocessing, visualization, clustering, and Enrichment. I hope it will be …
Trouble using get_raw() function in crossmeta R package to extract GEO data for differential expres…
written 6.2 years ago by gggdddcrossmeta •

Hello, I am attempting to perform meta-analysis from gene expression omnibus (GEO) data with [crossmeta r package][1] in bioconductor My issue is that when I …
DESeq normalized values and RNA-seq analysis in Galaxy
written 6.4 years ago by pbm11 •

Hello All I have list of DESeq normalized values from a published dataset in GEO. I want to analyze it and get differential expression of …
What is the possibility of replicates being different from other replicates of same sample?
written 6.5 years ago by Karma

I have analyzed the dataset of **GSE38132** from gene expression omnibus. The is from **cell line breast cancer ZR-75-1** which comprises of **9 conditions** with …
Automated tool for downloading Autism data from GEO on Humans
written 7.4 years ago by naseerkhan861 •

Is there some tool using which I can download all the Gene Expression data(Subjects and Controls) from GEO(Gene Expression Omnibus). For example I want to …
Splice site usage from RNA-seq data
written 7.5 years ago by Suicyte •

Is there an online resource or downloadable dataset that would give me data on splice site usage from published RNA-seq experiments? Ideally, I would like …
Galaxy Framework Direct File Upload To Data Library
written 13.9 years ago by Sam ad •

<p>I am newbie of Galaxy framework. I am a Python developer. I want to know if it's possible to directly upload file to data library …