GUI commercial software for 10x single cell gene expression analysis

Question

[firestar]

I have a collaborator at a hospital who is looking for a GUI software for analyzing 10X single-cell gene expression data.

Please let me know of companies and tools suitable for such analysis. Desktop application or cloud solutions are fine as long as it doesn't require coding skills.

Please don't suggest any R or python toolkits or shiny apps. They are not a solution for non-technical people.

And yes, I know loupe browser. It's not a fully featured analysis toolkit. It's just a little exploratory data explorer.

[yura.grabovska]

Can you provide more information on the use case? If they want to generate data for a publication I would argue that the majority of the GUI type apps are going to not be up to scratch with modern R/Python libraries and also generally be limited in features/performance. Single-cell analysis is a complex topic and it's easy to make wonky conclusions from wonky analysis.

[GenoMax]

Single-cell analysis is a complex topic and it's easy to make wonky conclusions from wonky analysis.

Let us set aside a discussion of open/closed source software. To be fair, wonky analysis is possible even with open source R libraries, if one is not experienced/careful. Not every person/location has access to bioinformaticians (or they may simply want to do the analysis on their own) and thus commercial software is an option.

Partek flow is using a standard single cell data analysis workflow which you can find detailed here: https://help.partek.illumina.com/partek-flow/tutorials/analyzing-single-cell-rna-seq-data They also have public white papers available about some of the methods: https://help.partek.illumina.com/partek-flow/white-papers If one wanted additional details then Illumina support is an email/call away.

Similar information (and bibliography) is available for CLC Single cell module in the manual: https://resources.qiagenbioinformatics.com/manuals/clcsinglecellanalysis/current/User_Manual.pdf

[firestar]

They have 10X cellranger output (ie; counts). They want to perform the standard sort of Seurat/Scanpy analyses: QC, filtering, integration, normalization, PCA, UMAP, DGE, GSEA. It's not just figures.

Answer 1

[GenoMax]

Cloud solution: Partek Flow (going to be called Illumina Multiomics at some point soon, Partek was purchased by Illumina a couple of years back) : https://www.illumina.com/products/by-type/informatics-products/partek-flow.html

Local desktop: CLC Single cell analysis module (part of CLC Genomics Workbench premium and other server solutions): https://digitalinsights.qiagen.com/plugins/clc-single-cell-analysis-module/

Answer 2

[Arup Ghosh]

Except for GSEA, the app from Nygen can perform most of the analysis using a tool similar to Scanpy.

Docs: https://www.nygen.io/knowledge-base

Tool: https://www.nature.com/articles/s41467-022-32097-3

[GenoMax]

Interesting pricing model : https://www.nygen.io/pricing Depending on user needs could be used (or certainly tested) for free. And this is a swedish company, which may be a plus for firestar .

Answer 3

[Nicole]

Many researchers use the CLC Genomics Workbench and Ingenuity Pathway Analysis. CLC can be used to do secondary analysis for your dataset and produce outputs such as UMAP/TSNE, gene expression overlay, dot plot, volcano plot, differential expression and more. IPA can be used to do downstream interpretation – pathways and networks analysis, comparing different cell clusters and more. Recorded webinars below for reference:

CLC Genomics Workbench https://tv.qiagenbioinformatics.com/video/103963966/single-cell-rna-seq-cell-hashing-1

Ingenuity Pathway Analysis https://tv.qiagenbioinformatics.com/video/96591324/single-cell-rna-seq-data-upload

Also, here are some publications you may be interested in looking at:
https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=%22clc+genomics+workbench%22+single+cell&btnG=