User: luke.zappia

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Posts by luke.zappia

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Answer: A: Splatter: How to simulate cells in different groups and different path at the sa
... At the moment the ideas of groups and paths are separate, so it is not possible to simulate them at the same time. It's a little had to say without knowing more about exactly what you want to simulate but you might be able to simulate something like what you want by playing around with the path par ...
written 2 days ago by luke.zappia0
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Splatter: How to simulate cells in different groups and different path at the same time?
... Received as GitHub issue https://github.com/Oshlack/splatter/issues/28 Hello, I found that I would simulate groups use splatSimulateGroups() and use splatSimulatePaths() to simulate the path, how could I simulate them at the same time? ...
splatter written 2 days ago by luke.zappia0
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Answer: A: Control group size
... Some of the parameters have changed in the latest release. You now want to use the batchCells and group.prob parameters. For example splatSimulateGroups(batchCells = 1000, group.prob(0.5, 0.3, 0.2)) would give you 1000 cells in three groups with probabilities of 0.5, 0.3 and 0.2. See the vignette an ...
written 14 days ago by luke.zappia0
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Control group size
... Originally posted on GitHub https://github.com/Oshlack/splatter/issues/27 I have been using the following code to simulate different groups of single cells": splatter_sim_1 <- splatSimulateGroups(groupCells = c(100, 100, 100, 100, 100), nGenes = 500, de.prob = c(0.05, 0.05, 0.05, 0.05, 0.05), d ...
splatter written 14 days ago by luke.zappia0
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Answer: A: Robustness of Splat cell grouping
... By setting nGenes=21 you are creating a simulation with only 21 genes, with the default differential expression probability (0.1) only 2 of these genes will be differentially expressed. Depending on the expression level of these genes and the random fold changes that are simulated PCA may/may not pi ...
written 5 months ago by luke.zappia0
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Robustness of Splat cell grouping
... RECEIVED AS A GITHUB ISSUE https://github.com/Oshlack/splatter/issues/16 Up/down regulation of random genes is working a bit weird. plotPCA(splatSimulateGroups(groupCells=c(1000,1000), nGenes=21), colour_by='Group') gives: whereas plotPCA(splatSimulateGroups(groupCells=c(1000,1000), nGenes=22), ...
splatter written 5 months ago by luke.zappia0
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Answer: A: Trouble installing splatter
... Yes you will need those versions of R/Bioconductor, I should have mentioned that in my answer. From a quick google I think those warnings are caused by objects in your workspace. I don't think they should effect your ability to use Splatter. ...
written 6 months ago by luke.zappia0
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Answer: A: Trouble installing splatter
... Hi It looks as though your problem is with the fields package rather than Splatter. From a quick look it seems like fields is designed for spatial data. It is not required by Splatter so you should be able to say no to updating fields without any bad effects (unless you are using it for something e ...
written 6 months ago by luke.zappia0
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Trouble installing splatter
... Question received via email: Hello! I have been having a really hard time installing splatter. I get a lot of errors saying splatter is not compatible with various versions of R.   Then after upgrading to R 3.4.0, I tried    biocLite("Oshlack/splatter", dependencies = TRUE, build_vignettes = ...
installation splatter written 6 months ago by luke.zappia0

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