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I am new to analyzing mass spectrometry data, so for my first experiment (an IP experiment with trypsin digestion), we let our mass spec core facility (the experts) run MaxQuant on the raw data for us…
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Hi, I was wondering if there was a way to change the clustering distance threshold that BINDetect uses to form motif clusters from the default (which I believe is 0.5)? If not, I believe it may be a u…
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Hi
I think that this protein is causing problems with the annotations. The transcript appears to encode for 2 proteins, one is a dbTF the other is described in UniProt as: Product of the upstream o…
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hello,Michael
Thanks for your wonderful software.
In recent days, I want to use it for my analysis. I had installed it very well follow your instruction.
```
$REforge.py -h
usage: REforge.py [-…
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The following terms have no annotations; 1 has a InterPro mapping; 2 have UniRule & HAMAP mappings, see
https://github.com/geneontology/go-annotation/issues/5345
@balhoff Can you please obsolete t…
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Hello @xindong95 , I'm interested in using SCRIP software to identify gene targets of some transcription factors that apparently have an important activity on my samples. I processed my scATAC-seq dat…
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e.g. the query
```SPARQL
SELECT DISTINCT ?item ?itemLabel ?_PubMed_ID
WHERE
{
?item wdt:P31 wd:Q13442814 ;
rdfs:label ?itemLabel .
OPTIONAL { ?item wdt:P698 ?_PubMed_ID. }
FIL…
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In the script `makefiles/05_integration.mk` I implemented the clustering of all the motifs discovered for a given TF, across all the data types. These give us an interesting selection criterion by ev…
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1. [x] Migrate the total annotations graph from old stats to new stats - "Cumulative annotations by type and year"
2. [x] Remove genes and annotations per paper from old stats - "Annotations/genes fo…