Comments (1)
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
The current version of the software is just designed for human and mouse. But the method could be used in other species. To apply this method, you need to construct a prior of RE-TG first. Once this prior is available, we can use the PECA method. In the future version, we will consider to include other species.
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Related Issues (14)
- matrix dimensions must agree error in matlab HOT 2
- non-model organisms HOT 2
- Using FPKM for PECA/TimeReg HOT 1
- Request for code clean-up and question about init. of "EM-like" approach HOT 2
- Remove assumption MATLAB is loaded via `Lmod` HOT 3
- Updates on `PECA` and related repositories HOT 2
- lack of CRS part
- Error- Couldn't open motif file
- Can we use multi-cores to run the programme? HOT 1
- Error when running 'install.sh' HOT 1
- Question: Do you suggest filtering the input gene expression table before running PECA HOT 1
- Undefined function 'fsolve' for input arguments of type 'function_handle' when running `PECA_compare_dif_multiple.sh`
- Question: should I use only nucleosome free region as ATACseq input? HOT 2
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