conos
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kharchenkolab
R package for the joint analysis of multiple single-cell RNA-seq datasets
Hi @VPetukhov @evanbiederstedt ### When creating a conos object the session crashes at: ``` Performing P2 processing... 12360 cells, 25732 genes; normalizing ... Using plain model Winsorizing ... log scale...
Hi @evanbiederstedt , Is there an equivalent function to this in Seurat https://github.com/satijalab/seurat/issues/3116#issuecomment-640440296 within conos.
Hello, I noticed that there was a new(ish) tutorial for performing conos with velocity information. It would be great if this was capable of working with "generic" h5ad files with...
Hi, This is not a question but rather a need for clarification. I am confronted with some limitations due the input data being Seurat objects. For instance, detection of gene...
Hi, Thanks for the great tool. Conos has been working fantastically on my dataset. I am writing as to ask whether it would be possible to obtain feature loadings for...
It should be possible to solve using graph coloring algorithms. For example, [MapColor](https://github.com/hunzikp/MapColoring) is a package, which does it for polygon maps (probably there is something better for our case)....
In function [getDifferentialGenes](https://github.com/hms-dbmi/conos/blob/master/R/conclass.r#L338) currently supports only pagoda2. To fix it, we need to create function `getDifferentialGenesSeurat` and call it conditionally in the same way as [`getDifferentialGenesP2`](https://github.com/hms-dbmi/conos/blob/master/R/conclass.r#L351). Function should have the...
I am opening this issue as a notification because `conos` is listed [here](https://cran.r-project.org/web/packages/Seurat/index.html) as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5...
Working with multi-modal data (e.g., 'CITE-seq + scRNA-seq' or 'TCR-seq + scRNA-seq') often produces joint dimensionality reductions (e.g., [MOFA2](https://github.com/bioFAM/MOFA2), [mvTCR](https://www.biorxiv.org/content/10.1101/2021.06.24.449733v2.full) or [totalVI](https://docs.scvi-tools.org/en/stable/tutorials/notebooks/totalVI_reference_mapping.html)). However, most integration methods can't work with those...
HI, Thanks a lot for supporting CONOS! I am back to using this great tool and try now function getPerCellTypeDE. It looks very promising but I cannot find the way...
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R package for the joint analysis of multiple single-cell RNA-seq datasets