neocaleb / tenet Goto Github PK

As told in #9, the mutlicore TENET and TENETsinglecore uses different indexes.
However, when converting the list of gene pairs into TE matrix, it works the same way as multicore TENET, subtracting 1 from the index.

This causes the singlecore TENET to break, as it puts gene pair [0,1] into [-1,0], yielding different results.

Also, singlecore TENET does not work with a , before the genes.

Hi,

I am wondering if it could be possible to use TENET with real time points rather than pseudo time information. In my case the vector of time points will only contain a few integer values that will be repeated for most cells.

Thanks for your help!
Ines

Hello,
I am doing application research on the reconstruction of gene regulatory networks and interested in the TENET algorithm. However, when I running the example data, the result matrix in TE_result_matrix.txt is all 0 for all pairs of genes. I am wondering should this output be all 0 for the example data? (or I make the mistake in running the code). Thank you so much for your help.

Hi there,
I'd like to ask that why there's difference between line 71-72 in TENETsinglecore and line 49-50 in runTE.py? It seems that they do the same thing.
Thanks

Hello,

Thank you very much for this program from the paper it seems like a great tool!

I was trying out to run it on a simulated dataset from DYNGEN with 500 cells and 100 genes however the program is still running after more then 18 hours now! This seems pretty long and I am afraid something went wrong. Or is it to be expected to run that long?

I am using 10 threads :)

Thanks for your help
Philipp

question about history length in file runTE.py line 69, its default value is 1, and I noticed that the max time point in the trajectory.txt is also 1. so can you explain more clearly what does this history length actually do? Thanks!

It is interesting to know the implementation of transfer entropy in the analysis of scrnaseq.

Do I need to use:

1. The discretization algorithm which convert the exp in to 0 and 1: if it is, what determines the threshold?
2. I have two trajectories from wishbone. Can I use the direct output from it?
3. Cell select txt file may require further description. How can I make the cell select file? Please let me know :)

Thanks!

Hi there,
we used the command
./TENET OB_temp.csv 10 OB_PAGApseudotime.txt OB_PAGAcell_select.txt 1

The input file included 3000 genes and 6424 cells.
We expected the matrix output file as usual. However we got
10 files called:
TE_out_aaa.csv
TE_out_aab.csv
...
TE_out_aaj.csv

They all look similar

1, 2, 0.00016435724617081058,0.00017018181705232195
1,3,9.219382988825285e-05,0.001077501635620558
1,4,0.00026165766902638675,0.0008222731935857703
1,5,0.0,2.0344534011729684e-06
1,6,2.1777893709535886e-05,2.2460595471730527e-05
1,7,0.0,0.0
1,8,2.1006674256813516e-07,2.100340090475586e-07
1,9,2.1006674256813426e-07,2.100340090475579e-07
1,10,1.400117626303666e-07,1.4001176263036658e-07
1,11,0.001054885122915543,1.105408979823489e-05
1,12,1.2648365209598076e-06,1.2616793584688755e-06

The last files ends with
2999,3000

It seems like those values depict the indices of the matrix. However, we would then expect only one value for each gene-pair.

Why there are two and why didn't we got the expected matrix output?

cheers

1. It would be better to explicitly use python3 instead of python since some computer often have python2 as default python
2. It seems like input files must be located within the current working directory. It would be convenient to allow input files in a separate folder for handling multiple different data sets.
3. openmpi dependency is not clear. at least it didn't work with openmpi3. I guess it's based on openmpi > 4.0?

I saw your bioRxiv preprint recently, and the work looks very interesting.

I am one of the developers of SINGE (formerly called SCINGE) and am wondering which version of the software you used and what hyperparameters you selected. Are these details in your manuscript or supplement? The SINGE performance was not great in your evaluation, and we'd like to diagnose what happened. Thanks.

1. in makeGRNbyTF.py
   Line 8:
   ifile = open("GO_symbol_"+species+"regulation_of_transcription+sequence-specific_DNA_binding_list_list.txt")
   ==> ifile = open("GO_symbol"+species+"_regulation_of_transcription+sequence-specific_DNA_binding_list.txt")

NumberOfLinks=sys.argv[2]
Line 42:
fdrCutoff=float(sys.argv[1])
==> fdrCutoff=float(sys.argv[2])

2. in makeGRNbyTFsameNumberOfLinks.py
   Line 6:
   ifile = open("GO_symbol_"+species+"regulation_of_transcription+sequence-specific_DNA_binding_list_list.txt")
   ==> ifile = open("GO_symbol"+species+"_regulation_of_transcription+sequence-specific_DNA_binding_list.txt")