kaizen89

Is there a way to determing the top genes driving the velocity?

2

Hi, I was wandering if it was possible to determine what are the top genes driving the trajectory based on the RNA velocity. Is there a way to do that?...

Failed to connect to cibersortx.stanford.edu:80: Connection timed out

1

I have an error that is probably related to proxy settings as the problem disappears when I connect with a private network. I've already set the proxy settings in Rprofile...

EcoTyper does not handle spaces in path names

2

I have a dropbox business account and I'm trying to run EcoTyper example tutorial but I get an error due to the dropbox root folder name containing a space, even...

How to force Monocle to use a specifc cluster as the starting/ending point

3

Hello, I am using Monocle2 and I want to order my cells allong a trajectory of activation, the problem is that I know biologically that one specific cluster shoud be...

find genes with expression in cluster A higher by a given FC than any other cluster

1

Hi, I was wandering if it was possible to add a feature to find genes with an expression in cluster A , let's say 2 times higher than any other...

question regarding abundance table

2

Hi, I am wandering what does the abundance table exactly refer to, is it abundance of cell states among each cell type or is it among all cells. On my...

Hi, It would be really nice to add a function to plot let's say proportions of tumor vs normal tissue for each cluster but after mormalizing by group count (tissue)...

Hi, In my analyses I usually exclude genes that I consider as Junk and not biologically meaningful. Is there a way to exclude such genes contained in a text file...

``` HGNChelper::checkGeneSymbols("mt-Nd2", species="mouse") Maps last updated on: Mon Apr 4 17:31:23 2022 x Approved Suggested.Symbol 1 mt-Nd2 FALSE AU018611 Warning message: In HGNChelper::checkGeneSymbols("mt-Nd2", species = "mouse") : x contains non-approved...

what information should be in the cell_type column?

2

Hi. I have a count dataframe to which I added the cluster information to the cell_type column. However the DEG function ecaluates `length(unique(data$cell_type))` and stops if different than 1. does...