Zhana Duren
Zhana Duren
Yes, PECA is still active and undergoing maintenance. I apologize for not seeing your comments earlier as I have been on summer vacation. Please review all my previous responses to...
Thanks. The eita0 and eita1 parameters were learned from "EM-like" approach PECA model. This is the code for PECA2, which do inference by refining parameters based on the pre-trained PECA...
For differential expression analysis, people did use count based method like DEseq2 and EdgeR for many years. However, those methods are worse than the simple ranksum test, which take FPKM...
Currently, the PECA software prior dataset does not contain non-model organisms. However, if large scale paired gene expression and chromatin accessibility data is available, we can build a prior data...
It looks like the gene name variable is empty, please check your input file of gene expression, the gene name has to be the official gene Symbol, and the data...
It might be a version problem, I did some changes. Please update the codes under scr folder and try again the RAd4 example. https://github.com/SUwonglab/PECA/tree/master/scr
I think the problem is solved, you can run the fifth step now.