Tempora
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BaderLab
Pathway-based trajectory inference method for time-series scRNAseq data
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...
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...
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...
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)) ) ```
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 =...
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...
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...
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!
