floklimm / scppin Goto Github PK

Hi!

I am struggling with installation of scPPIN and dapcstp libraries, usual way trough devtools::install_github or cloning from github didn't work ("Error: Failed to install 'unknown package' from GitHub").
I would appreciate any help.

Best,
Irina

Dear,

I am very eager to try this tool. However, I have no clue how to install. Is it possible for you to make a simple installation guide for major platforms such as Ubuntu in my case?

I guess I will not be alone in this need as many of the users will be biologists with minimum understanding of command line and a decent understanding of R.

Or Can I just run the .R file after installing the dependencies?
It will be great if you can include installation steps in the homepage.

Thanks and kind regards,
Saeed

Hi,

I tried the webtool. It returns error
'An error has occurred. Check your logs or contact the app author for clarification.'
I used a csv file as attached. I tried the csv file in a few different format, eg. by using log10 values of P values instead of p values themselves as you have shown in the 'example_files' in this repository.

Can you kindly let me know what is going wrong. I attached xlsx here as csv is not supported for attachment.

scPINN_cluster0.xlsx

Thanks

Hi,
I have been try to identify the most optimal Functional modules for all my cell types. however when i run the function detectfuncitonalmodule for some of my cell types , that have a high number of genes with pvalues (n=3000) , dapcstp gives an error as below
Error in if (is.numeric(v) && any(v < 0)) { :
missing value where TRUE/FALSE needed

is this because it couldnt find an optimal soultion at the particular FDR or is it to do with my data?

again the checksum test you have suggested returned 0.

Thanks some insight into what this error means in terms of identifying functional modules would be great!

Best,
Devika

Hi,

You should use system.file('extdata', 'biogridHomoSapiens3.5.166.graphml', package='scPPIN') and not "./inst/extdata/biogridHomoSapiens3.5.166.graphml" to find the file in loadPPIN.
The relative path specification only works if you run the function from the main folder.

Another think you could consider doing is having the R/ folder as a submodule so that it can be installed directly using 'devtools::install_github()'.

Hello,
I have successfully compiled dapsctpMAC , as i can use it in the terminal and see the help options. however R cannot seem to locate the solver. Where does scPPIN expect the executable to be located? is there a way to see my own path to the executable on my system?

I tried putting a copy in the R directory of the package but that dint work. Perhaps its something simples and i am missing the obvious. But some help will be great!

Thanks,
Devika

Hello,
I have been trying to run FitBum function on the Pvalue vector for a particular cell. It keeps saying optimization failed. In the FAQs there is a solution in regards to pvalues not being in the 0-1 interval, but i ran the checksum test suggested in tutorial 1 and that returned a value of 0L.

So what might be the reason for this.

Best,
Devika

Hello,
sorry it isnt clear how best to install scPPIN . Do we install it via R or do we download the pre compiled source files and then point to the relevant directory for R to install it.

some help would be appreciated!

Thanks,
Devika