Question: Looking for publicly available dataset.
0
gravatar for KVC_bioinfo
13 months ago by
KVC_bioinfo350
Boston
KVC_bioinfo350 wrote:

Hello All,

I am trying to find a gene expression dataset which is publicly available? I am looking for gene counts coming from HTSeq like tools for different genes. This is not specific to any genes. It can be from human/mouse. I want the dataset only to test few statistical tests.

The purpose of this is for use in a project at University.

Could someone help me suggesting sources for such datasets?

Thanks!

public dataset • 515 views
ADD COMMENTlink modified 13 months ago by mark.ziemann1.1k • written 13 months ago by KVC_bioinfo350
1

Have a look at the recount2 R package, lot's of data readily available.

ADD REPLYlink written 13 months ago by WouterDeCoster35k
1

ArrayExpress has number of processed data and filtering option may show dataset you are looking for.

ADD REPLYlink modified 13 months ago • written 13 months ago by rice.researcher130

Thank you so much. I will look into it.

ADD REPLYlink modified 13 months ago • written 13 months ago by KVC_bioinfo350

No. But I will definitely look into it.

ADD REPLYlink written 13 months ago by KVC_bioinfo350

Hi! I am new to RNA-Seq. ARCHS4 seems a great platform. May I ask a naive question? For the gene counts data that we download from ARCHS4, do I have to convert them to FPKM, RPKM or TPM before I do gene expression analysis between different samples?

Thank you!

ADD REPLYlink written 6 months ago by bunnyslope0
1

Best to open a new question - I'm sure the community can help you with your request :)

ADD REPLYlink written 6 months ago by mark.ziemann1.1k
3
gravatar for mark.ziemann
13 months ago by
mark.ziemann1.1k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.1k wrote:

2 good options:

recount2 https://jhubiostatistics.shinyapps.io/recount/

ARCHS4 http://amp.pharm.mssm.edu/archs4/

Also many GEO series include count matrices although these are generated by various pipelines.

ADD COMMENTlink modified 13 months ago • written 13 months ago by mark.ziemann1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1666 users visited in the last hour