suwonglab / peca Goto Github PK

Thanks for the software.

I'm currently having issues running the 'install.sh' script. Attempting to download the tar.gz file from your website returns a 403 Forbidden error. It looks like the entire website has access permissions removed completely. Full error below:

--2021-10-06 18:42:01-- http://web.stanford.edu/~zduren/PECA/Thresholding-Based%20SVD_files/Prior.tar.gz
Resolving web.stanford.edu (web.stanford.edu)... 171.67.215.200, 2607:f6d0:0:925a::ab43:d7c8
Connecting to web.stanford.edu (web.stanford.edu)|171.67.215.200|:80... connected.
HTTP request sent, awaiting response... 403 Forbidden
2021-10-06 18:42:01 ERROR 403: Forbidden.

tar (child): Prior.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now

Thank you!

Hi there,

I've been exploring a bunch of repositories that either contain the PECA software or have PECA as a major dependency. I've found these repos across a few accounts:

1. PECA by SUwonglab
2. PECA by durenzn
3. PECA-1 by durenzn
4. TimeReg by SUwonglab
5. vPECA by AMSSwanglab

I've previously submitted issues on the SUwonglab/PECA issue tracker and made an attempt to get in touch with @durenzn directly, both via "@" and by email. Unfortunately, those issues are still awaiting responses.

To get a better picture of the current state of PECA and cast a wide net, I'm posting this identical issue across all these repositories. Is PECA archived, or is it still under development or maintenance? If it's still being developed or maintained, where's that mainly happening?

Any information or guidance would be super helpful. Thanks!

Hi, I have gone through the PECA pipeline without ENCODE. But I don't find the result related to CRS mentionded in TimeReg article, neither in the source code. It is supposed to build a curated network based on TRS and CRS filtering according to the article. But I find the RE-TG pairs in the present pipeline are simply identied by overlap with prior data, which is generatted by a linear model in our cases.
Is it my misunderstanding?

Hi，
Can non-model organisms use this tool to infer networks?
Thanks a lot for your time and effort!

The manual says PECA can use TPM or FPKM as input but FPKM values are not usually used to compare between samples. Is it ok to use FPKM if we intend to use compare_diff or TimeReg, which compare between samples? (Also, for TimeReg, we have to take averages of the RNA replicates, can we do this with FPKMs? Or should we take the averages of the counts first then convert to FPKM?)

Hi, I was wondering if filtering the ATACseq bam file used as input for PECA2 to retain only Nucleosome Free Regions is required and or would increase the accuracy of the analysis.

When running PECA_compare_dif_multiple.sh I got the following error:
Undefined function 'fsolve' for input arguments of type 'function_handle'.

The fix (for me) was to install the MATLAB 'Optimization Toolbox'.

System: MacOS Monterey (12.2), MacBook Pro 2020 (Intel i7)

Hi,
I read this paper "Modeling gene regulation from paired expression and chromatin accessibility data" and found this software will be very helpful for my research. My research organism is Amphimedon queenslandica (one kind of demosponge). I have the ATAC-Seq data and RNA-seq data. We have the genome and genome feature formate files. I want to know how could I use PECA for my analysis? I found this software only build in human and mm information.
Thanks for any useful information advance.

Best Regards
Huifang

Thanks for your software.

I have a batch of Time Course ATAC and RNA-seq data to run.

Accordingly, i am running the PECA first. The motif finding step is too slow. I tried to add "-p 48" following -size given, however, it seems not work.

PECA's shell scripts assume Lmod is installed and that MATLAB is available via Lmod in a module named matlab. See e.g. here.

This info is missing from the documentation, but this dependency/assumption should in any case be removed.

Hi, I ran the example file and everything seems to work fine.

However, when I tried with my own samples I get an error in Matlab

"matrix dimensions must agree"

the line of code that causes the error is

Score=sqrt(TFExpG').(2.^abs(R2)).*full(BOH);

Removing .*(2.^abs(R2)) allows the line to execute without errors.

Any ideas as to where the problem might be?

Thanks,
Sky

Hi team,

I read in the manuscript you mentioned building the network considering only genes with FPKM > 10.
So do you suggest removing lowly expressed genes before running PECA?
In addition, I noticed in your /Prior/TFTG_corr_mouse.mat, there is no Trp53 for mouse TFName, just want to know how you defined these TFs?

Thanks.

Hi, Thanks for the nice approach and follow ups TimeReg and vPECA.

1. Gentle request for code clean-up: It would help open source development for some minor clean-up (var names, comments, typo fixes, ...). Then other devs could more easily work on larger refactorings, e.g. the abstraction of PECA/scr/PECA_network_* functions and so on.
2. Can you describe the initialization strategy for your "EM-like" approach? For instance, I see here you fix eita (eta, $\eta$ ?) to two values:

eita0=-30.4395;
eita1=0.8759;

I'm surprised single values are fixed and fixed to 4 decimal places for this algorithm.