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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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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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**Hello Tim and team,**
**As always thanks for your excellent work. I am in the process of using Signac to analyze some scATAC data and found the ClosestFeature function gave the following error:**
…
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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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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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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…