Francesco G. Brundu

I am trying to use finalterm under Ubuntu 12.04. When I start it, it crashes when I insert a character. Starting from another terminal I get: ``` /media/data/git/(branch:master*) » finalterm...

How to change font size in theme?

5

Hi, I am trying to change font size of interface text. I was searching for the `.sublime-theme` file for spacegray (I read this https://www.sublimetext.com/forum/viewtopic.php?f=2&t=7411 ) but I am unable to...

I have a doubt on how to properly use pySCENIC and iRegulon. I am comparing two conditions, Case and Control, and I want to test two possible analyses: - Differential...

Plot cell_metadata along pseudotime

1

Hi, Is there a way to plot a specific cell_metadata column (e.g. a cell score for a specific process) along the pseudotime, in a similar fashion to the [plot_genes_in_pseudotime](https://rdrr.io/bioc/monocle/man/plot_genes_in_pseudotime.html) function?...

Hi all, is it possible to make the `about.md` page as the default page? Thanks, Francesco

How to call combat.py with no covariates

4

Hi, I am trying to use your script passing an expression matrix in dat and a sample information file on batch.. I do not want to pass any covariate, but...

Run with 47K rows, 566 columns and 48 batches takes 5+ hour and it's still running

2

I am running combat.py and I don't know if it is normal that with 47K genes, 566 samples and 48 batches it is taking more than 5 hours to terminate....

PR for `draw` method for additional figure aesthetics: - Figure title and font properties - Figure frame removal flag Example code: ``` c.draw('Gran', ccmap='Reds', weight=2, dpi=200, figsize=(5,5), lw=1.0, title='Gran', font_props={'fontname':...

Unable to draw more than one gene in the same plot

2

Hi, I receive the following error while trying to draw a list of genes, probably due to changes in the underlying matplotlib API: ``` c.draw(['GRIA1', 'SLC1A3']); --------------------------------------------------------------------------- AttributeError Traceback (most...

PCA, "RuntimeWarning: divide by zero encountered in log" and wrong PCs ordering with svd_solver arpack

3

Hi, I am trying to evaluate a PCA on a dataset with a very low number of Principal Components. I am getting the following error when trying to plot the...