Job:Bioinformatics consultant recommendation needed: mouse RNA-Seq, oncology related

Question

[parismj]

First post here. Looks like a great community.

I work for a biotech. I have an 8 sample RNAseq data set that I need help analyzing for DGE pathways and unique SNP's. Many more details are available, but let's keep it simple for now. I'm looking for a recommendation for a professional organization to contract with that has the skills, the access to software and the scientific background (oncology) to help me dig deeply into the data.

Thanks in advance for your help.

[Michele Busby]

Next time, it is better to talk to your bioinformatician before the data is run. We can help a lot with design optimization.

[parismj]

Should have mentioned. Species is mouse. Strain is balb.

Thanks anyway "keygene."

[russhh]

are you looking to be trained to analyse your own data or someone to analyse your data for you?

[mikhail.shugay]

Usually the company that performs high-throughput sequencing and library prep (the one you've got the data from) offers bioinformatics service with some discounts. Are you going to perform similar analysis later? If yes, then it is better to learn by yourself by trial and error (and asking questions here) or hire a bioinformatician.

Answer 1

[Jeremy Leipzig]

https://www.elance.com/r/contractors/fbk-0/q-rna-seq%2C%20bioinformatics

[parismj]

Thanks for the link Jeremy. Looks like there are some inexpensive freelance hands available out there. What I'm missing however is a recommendation for either an individual or organization as per the title of this thread. Anyone is welcome to contact me directly if there's concern about disclosing a personal opinion in a public forum (parismj - at - gmail). Thanks!

[Istvan Albert]

Mikael Huss on that list definitely knows bioinformatics, check out his blog (he has co-authored a book on RNA-seq)

http://followthedata.wordpress.com/

Answer 2

[EdgeLeap]

Dear parismj,

We are EdgeLeap (http://www.edgeleap.com), a Dutch SME with a mission to help people to dig deeply into the data - and get the relevant knowledge out. We provide different types of bioinformatics services (which would cover analysis of your dataset), but our specialty is making complex data interpretable through pathway and network analysis. We can help you to analyse your data in the context of external information such as pathways, cellular location, literature evidence, other parameters/clinical outcomes in your study etc. - which is a valuable add-on for e.g. prioritization of targets/markers. If this sounds relevant check our profile at http://www.edgeleap.com or just get in touch to see how can contribute.

Answer 3

[Coryza]

Hi parismj!

If your dataset is plant related; take a look at our company! (I guess it's not, since you've mentioned oncology)

http://www.keygene.com/products-tech/

Answer 4

[David Langenberger]

Dear parismj,

We at ecSeq Bioinformatics have quite some background in the analysis of RNA-Seq cancer data (find here a list of publications of projects we were involved in). In our team there are computer scientists, bioinformaticians and medical doctors. Altogether, we are able to provide an all-round carefree package for the problem you mentioned.

Feel free to take a look at our website and if you are interested, you can contact me directly and we can chat a bit about your project.

All the best,
David
Website: www.ecseq.com