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SUwonglab/PECA
lack of CRS part

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 ...
  • lizihe21
  • Opened 
    on Nov 6, 2023
  • #18

SUwonglab/PECA
Updates on `PECA` and related repositories

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. ...
  • t-silvers
  • 2
  • Opened 
    on Jul 31, 2023
  • #17

SUwonglab/PECA
Remove assumption MATLAB is loaded via `Lmod`

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 ...
  • t-silvers
  • 3
  • Opened 
    on Jun 30, 2023
  • #16

SUwonglab/PECA
Request for code clean-up and question about init. of "EM-like" approach

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, ...
  • t-silvers
  • 2
  • Opened 
    on Jun 30, 2023
  • #15

SUwonglab/PECA
Using FPKM for PECA/TimeReg

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 ...
  • Chloe-Thangavelu
  • 1
  • Opened 
    on Feb 23, 2023
  • #14

SUwonglab/PECA
non-model organisms

Hi， Can non-model organisms use this tool to infer networks? Thanks a lot for your time and effort!
  • liyangyang12
  • 2
  • Opened 
    on Nov 7, 2022
  • #10

SUwonglab/PECA
Question: should I use only nucleosome free region as ATACseq input?

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.
  • ftucos
  • 2
  • Opened 
    on Oct 5, 2022
  • #9

SUwonglab/PECA
Undefined function 'fsolve' for input arguments of type 'function_handle' when running `PECA_compare_dif_multiple.sh`

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 ...
  • ftucos
  • Opened 
    on Jun 14, 2022
  • #7

SUwonglab/PECA
Question: Do you suggest filtering the input gene expression table before running PECA

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 ...
  • alexyfyf
  • 1
  • Opened 
    on Dec 19, 2021
  • #6

SUwonglab/PECA
Error when running 'install.sh'

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 ...
  • kevinqiu0
  • 1
  • Opened 
    on Oct 6, 2021
  • #5
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