ouija

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Apologies in advance as I realise this is partially a clone of https://github.com/kieranrcampbell/ouija/issues/5. But I'm looking for several of the functionalities of ouija, but with a precomputed pseudotime from another...

skannan4

Can't load sce data

30

Hi, I am new to Ouija but quite excite about using it. I have got my Seurat object transformed into a singleCellExperiment object. Unfortunately Ouija doesn't seem to see like...

JihedC

Pseudo time as function of a predefined group of genes

3

Is it possible to plot the cells as a function of a list of genes?

kvshams

Inference without modeling dropout?

2

Hi Kieran, thanks for the cool package. I am interested in learning more about Bayesian stuff so your other work seem interesting as well! Recently there has been talk about...

mochar

Neverending sampling chain 1, cycling CPU

1

Hi Kieran, Thanks for developing ouija. I'm testing it out on a complete 1386 cell x 28000 gene matrix of single cell RNASeq counts. I tested 200GB-1T memory and 1-4...

cemalley

Error in svd when response_type="transient"

3

Firstly thanks for adding the transient option! However, when response_type="transient" i.e. no genes are designated switching svd throws an error: ``` library(ouija) data(example_gex) oui

daniel-wells

Unclear licensing terms

3

Please add a `LICENSE` (or `LICENSE.md` or `LICENSE.txt`) file to the repository, ideally using an OSI https://opensource.org/ approved open source licence compatible with the wider R Bioinformatics community to maximise...

peterjc

Ouija not working w/ SCESet object

1

Exciting to try this out! I didn't have any joy though, applying ouija to an SCESet object (see attached pic). Looks like ouija could be clobbering the scater NAMESPACE on...

davismcc

Initialise all parameters from PCA etc to save MCMC runs

kieranrcampbell