Bioinformatics software for single cell omics

Question

[jackson9]

My professor asked me to find a software solution to deal with scRNA data analyses (preprocessing and analyzing data). The department is going to have VIZGEN and COSMX machine coming next quarter. 3-4 labs depend on 1 bioinformatician guy is really annoying and inconvenient.

There are some companies I am looking at:

• BioTuring
• Rosalind
• Cellxgene

Most of the time, we want to compare between metadata categories to generate insights, and also apply gene set / pathway analysis on those. Any suggestion on that?

[ATpoint]

Ask for demonstrations, let them show the software, then try it yourself. If they don't offer demos and free trials then they're out imo.

[jackson9]

great idea. Idk why I forgot about this LoL. going to registering all of them now.

[Ram]

Any suggestion on that cause I am truly depressed rn :(

Setting aside the fact that we don't need to know how you're feeling and cannot genuinely help you with that, please avoid IM jargon like "cause" and "rn". Use professional language - "because" and "right now". I've edited the sentence above to make it look a little professional.

[yl759]

If you are willing to consider analyzing it on your own, Seurat has a solid setup, and Scanpy is becoming popular if you like using more Python-based tools. You're always welcome to ask questions on this forum!

[jackson9]

Previously, all the lab members tried to learn to perform things with Seurat and Scanpy, but eventually ended up with messy (sad). That's why I'm looking for a bioinformatics solution for biologists like us.

[jackson9]

Have a demo with BioTuring today.

• They have exactly what I need: metadata composition, single-cell GSEA (AUCell), pathway (wikiPathway - basic one).
• The image interactive analyses of Visium and COSMX was impressively fast.
• So many other features than cannot convered in 30 min demo. I was offered 1 month-trial. Price will be sent in followed up email

Tomorrow will be Rosalind, will update later...

Answer 1

[fracarb8]

If you want to have a framework for both visualisation and data processing you should check the QIAGEN OmicSoft family of tools. I used Oncoland in an industrial setting, and it was great to share data with biologists and allow them to play with the data themselves. You can go from fastq.gz to dataset integration with few clicks, and integrates quite well with IPA (same company). They also have a scripting language which is terrible to use, but handy to automatise the pipelines. The drawback is that it can get quite pricey.

[jackson9]

Wow, never heard about this before. I will absolutely take a look at it. Thank a lot

[GenoMax]

OmicSoft may be significantly more expensive for a small group. CLC genomics workbench is desktop software but it requires an extra cost plugin to do single cell data analysis. On whole Qiagen software can be pricey as already noted.

Answer 2

[GenoMax]

Take a look at Partek Flow if you want spatial data analysis as well: https://www.partek.com/ End-users can use this software freeing up your time for other things.

Answer 3

[Claire Watson]

Rosalind supports wide range from fastq to expression matrix. They also support bulk rna and ATAC data. BioTuring only supports from expression matrix (so, no fastq). Seem like the analyses are around single cell omics (scRNA and sc-spatial like COSMX, VIZGEN, VISIUM,...), so no bulk rna and ATAC and others. To me, rosalind support wider ranges of data format, given more flexibility in input datasets format, but BioTuring are more user friendly and provide deeper analyses in its supporting format.

GSEA and pathway analysis are available in BioTuring and their speech is really impressive.

[jackson9]

Nice. As your suggestion then BioTuring solution is more suitable for my lab. Any idea about its price?

[Claire Watson]

We bought group license and it's quite reasonable but I'm not sure about individual license. You can contact them for trial and demo, they will show them more details

[Ram]

The spam bot accidentally classified your post as spam and banned you - I think some keywords in your posts may have triggered this action. I've restored your posts and opened your account; sorry for the trouble!