Human Reference Matrix for Tricycle library to predict cell cycle phases
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20 months ago

I'm utilizing the Tricycle library found at this link.

I need to predict the cell cycle phase using the project_cycle_space function, which you can review here.

Here's the function syntax:

project_cycle_space( x, exprs_values = "logcounts", altexp = NULL, name = "tricycleEmbedding", ref.m = NULL, gname = NULL, gname.type = c("ENSEMBL", "SYMBOL"), species = c("mouse", "human"), AnnotationDb = NULL )

I'm having difficulty with the ref.m argument, which expects a reference matrix. By default, it's set to mouse, but my data is human. Could you assist me in creating or obtaining a reference matrix for human? I've been struggling with this for quite some time. Thank you.

Tricycle scRNA-Seq R Single-Cell-Sequencing Cell-Cycle • 649 views
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Entering edit mode
20 months ago
ATpoint 88k

Please read the manual, it's in the appendix on the very bottom of https://www.bioconductor.org/packages/release/bioc/vignettes/tricycle/inst/doc/tricycle.html

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