Tempora

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Cholmod error 'problem too large'

2

Hi all, I'm getting the following error when trying to create the Tempora object with ImportSeuratObject: ``` Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line...

sciotlos

No significant time-varying pathways in MouseCortex Data

2

Hi, i have been trying to test Tempora on the `MouseCortex.RData` object, running the commands listed on the Readme.md page. However, after running IdentifyVaryingPWs, the function calls returns that there...

mjoppich

In the process of integrating Tempora with SCHNAPPs I implemented these changes. Only one was really required the fork (issue #17) the others are visual improvements or speed-ups. Thanks for...

baj12

getMD from SingleCellExperiment object

1

I am working with SingleCellExperiment objects. It seems that SingleCellExperiment::colData returns a "DFrame" and that reshape2::dcast in CreateTemporaObject requires a data.frame. ``` suppressMessages( setMethod("getMD","SingleCellExperiment", function(x) SingleCellExperiment::colData(x)) ) ```

baj12

CalculatePWProfiles issue - invalid class "GeneSetCollection" object

1

Hello again, After correcting the CreateSeuratObject issue, I've run into the following issue when calling CalculatePWPProfiles as: ``` CalculatePWProfiles(temporaObj, gmt_path ="Human_GOBP_AllPathways_no_GO_iea_January_13_2021_symbol.gmt", method="gssea", min.sz = 5, max.sz = 200, parallel.sz =...

sciotlos

Hello and thanks for the interesting tool. I am wondering whether we would be able to use this tool after clustering time-series CITE-seq data with Seurat using a method like...

rbatorsky

problem with running CalculatePWProfiles

3

Hi, I am trying to run Tempora on my dataset. I downloaded the right .gmt file(s) for mouse but keep getting error when running CalculatePWProfiles: `Calculating cluster average gene expression...

nmalwinka

Hi, Is this package compatible with Seurat v5 objects? If that's the case, which assay and slot should be used in the 'ImportSeuratObject' function? Thanks!

hernandezvargash

hello could you give data processing section code? I need to use based on your work. How can I get clusters' label? Your work is good. Thank you very much,...

Starsm7