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Hello, when I test `EAGLE.pl` on my computer (Ubuntu 18.04, MATLAB 2019b, perl 5), I met the following errors:
```
user@ubuntu:~/Github/EAGLE$ perl EAGLE.pl -E inputexample/cell_enh.bed -G inputexam…
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Hi,
Thanks so much for making this code available and usable!
In your NG manuscript, you look at some different options for using H3K27ac HiChIP, as well as including quantitative DHS signal. …
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I've increased the [description column](https://www.synapse.org/#!Synapse:syn21895659/tables/) to 1000 chars, but some new descriptions are way over that limit in the merged datasets table:
```
1 …
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Hi!
I can't seem to find the descriptions for the column names for the data frame returned by getAnnotation(GRset). The column names are fairly descriptive, but I would like to get more details. For …
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http://www.sequenceontology.org/browser/current_svn/term/SO:0000165
defined
A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientat…
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When running ananse network I've supplied a single gene expression file formatted as described, however I get this error:
ananse network -e tpm.txt -b binding_output.txt -o network_output.txt -a ~/…
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Summary of email to 14 Feb 2019
Astrid:
>Did we get suggestions yet from the ‘gene regulatory region’-experts on which ontological terms and hierarchies (DAGs) we should create for the regulatory …
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File:
ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.PRJNA13758.current.gene_product_info.gpi.gz
Some of the description lines include newl…
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Hi Colin
https://pubmed.ncbi.nlm.nih.gov/18270511/ confirms RBP2 (KDM5A, P29375) binds a 6 base motif CCGCCC, has enzyme activity and regulates transcription. In November I annotated this as a dbTF…
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You function do a lot, but what and how they do it is not explained, making it almost magic unless you delve into the code!
Here are some places in the documentation that might need improvement fro…