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Is there a way to run PePr without specifying input files, as is the case for analyzing ATAC-seq/DNase-seq data?
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(I received this question by email, and am including it and the response below - jmg)
I read your work on improved peak calling with MACS2. I belong in the
worst category and have been running MAC…
jsh58 updated
5 years ago
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Dear developers,
I wonder if there is documentation/example for training based on Dnase/ATAC-seq input? I would highly appreciate suggestions on parameter tweaking!!
It seems ATAC/Dnase are supp…
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Hello, after reading your article I still have some questions about what "label embedding" is. The introduction of "label embedding" in the thesis is not much. Is it another kind of sequencing data be…
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1. [Integrating ChIP-seq with other functional genomics data](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5888983/pdf/ely002.pdf)
2. [2014-nature review-Identifying and mitigating bias in next-gener…
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- https://github.com/ENCODE-DCC/rna-seq-pipeline
- https://www.genome.gov/sites/default/files/Multimedia/Slides/ENCODE2016-ResearchAppsUsers/ENCODE2016_strattan_slides.pdf
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Hi! I have tried to train the Leopard model only on the DNA seq of reference genome and remove the DNase-seq / delta DNase out from the input feature. However, the prediction result only gives the val…
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https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runMACS.R#L32
According to the [MACS2 page](https://github.com/taoliu/MACS) the settings
```--shift -100 --extsi…
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Hello. Your code **dataset.py** shows the process of building your data. However, you don't seem to have given a simple example to show temp_seq, temp_dnase and temp_labels. e.g. what kind of informat…
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Remove the "SELEX", "WGS", and the empty artifact. Check how many records are in SELEX and WGS first before removing and post this info here (with a date/timestamp when you retrieved these record…