johnmous/singlecell

Ovary single cell RNA-seq analysis workflow

Workflow in R used for ovary single cell RNA-seq analysis

The conda environment is also provided to ensure reproducibility of the analysis

Analysis was run on a computer cluster running Ubuntu 14.04 LTS

singlecell's Issues

an error in running FindVariableGenes

I try to repeat the result and I meet some problems.

error occurs there:
ovary <- FindVariableGenes(object = ovary,
mean.function = ExpMean,
dispersion.function = LogVMR,
x.low.cutoff = 0.1,
x.high.cutoff = 5,
y.cutoff = 0.4)

I get this:
Calculating gene means
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in seq.int(rx[1L], rx[2L], length.out = nb) :
'to' must be a finite number
Calls: FindVariableGenes -> cut -> cut.default
Execution halted

It's really strange. I first suspect there're error in parameters, yet I tried many ways including using all default / giving the only infinite default parameter, y.high.cutoff, a finite value, there is still this error. There's nearly no difference in the code, except that the provided data is h5 files so the reading is different, and working environment may be different, I run r program directly in linux.

I also put it on seurat issues: satijalab/seurat#5665

Thanks for any help!

Data....

It is kind of you to provide the walk-through, but it is challenging without the data files or sample file....

Where is the code about diffusionmap and monocle trajectory analysis

Hello,
I read your R script about single cell RNA-seq analysis workflow.But I can't find the code about diffusionmap and monocle trajectory analysis.I'm interested in it.Can you share it on github?