Visium data analysis software supporting deconvolution analysis
Hi all,
Does anyone have recommendations for software that supports Visium data deconvolution analysis? Thank you in advance
• 1,400 views
•
link
updated
by
jackson9 •
•
written
by
Claire Watson •
•
written
by
Claire Watson •
2 answers
There are no shortage of these, including those that require a reference and reference-free options. I have never used any of them, so I have no recommendation.
Plenty more available via ye olde Google.
• 0 views
•
link
written
by
jared.andrews07
I used BioTuring. They has good training models (this compapy started with scRNA, so they has lots of reference datasets). Cell2location is also implemented in the app.
• 0 views
•
link
written
by
jackson9 •
Log in to answer this question.
More posts like this
-
Creating a Single-Cell Signature Matrix for Bulk RNA-seq Deconvolution
written by Lloyd98 •
-
Deconvolution: bulk and cell signature data from different platforms or technologies
written by zhang.jianhai •
-
Forum: Cataloguing available spatial transcriptomics tools, then linking them together into a workf…
written by LauferVA
-
RNA-seq deconvolution algorithm that takes into account weight of marker gene
written by CTLong •
-
Visium deconvolution reference datasets
written by Claire Watson •
-
Visium spatial transcriptomics - mouse + human xenograft
written by Sy80 •
-
Copy Number analysis in 10X Visium data
written by kgiannikou •
-
Partial Genome alignment
written by hunterkwalt •
-
Software for detecting structural variation in bacterial genomes
written by michael •
-
Forum: Data Vizualization or Pathway Analysis
written by quevedo.marisa •
This is likely a bleeding edge subject so things will be rapidly moving. I see the following
https://github.com/kpcoleman/SpaDecon
https://github.com/RubD/Giotto
A comprehensive list of 15 tools in table 1 of this paper: https://www.sciencedirect.com/science/article/pii/S200103702200558X