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Hi,
I wanna know if this tool can be used for drosophila samples? Like the -n parameter, can it identify genes from different species or the FlyBase gene ID?
Thanks!
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Hi Simon,
great tool, I missed using it!
any chance you have a Drosophila/arthropods/insects/invertebrates version of the clustered vertebrate motifs like gimme.vertebrate.v5.0?
Or a code templ…
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- [x] _Acromyrmex echinatior_
- [ ] _Acyrthosiphon pisum_
- [x] _Atta cephalotes_
- [ ] _Linepithema humile_
- [x] _Pogonomyrmex barbatus_
- [ ] _Apis mellifera_ (HymenopteraBase)
- [ ] _Drosophila me…
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Experimental evidence violates taxonomy constraints
PTHR10997 Warning Experimental evidence IGI,IMP to PTN000108260 for annotation 385617457 to term GO:0016203 with species Drosophila melanogaster vi…
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In concert with with miRNA/transcription working groups.
- [ ] Terms to describe molecular functions of lncRNAs (see GO ontology tracker)
Review all long non-coding RNAs in D.mel and annotate
- […
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Open for discussion:
As the data retriever grows to support various formats of datasets. We could provide support for Sequence data.
From a quick search, I have come across some resources that we …
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I'm wondering what the best way to build a taxonomy for use in phyndr. I can retrieve for each species in the tree a lineage from domain to species, but they will be extremely variable in the number o…
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e.g. sleep
-increased/decreased total sleep (time spend asleep over total time)
-increased/decreased bout number
-increased/decreased bout duration
see https://github.com/FlyBase/drosophila-phen…
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It looks like there might be an issue with the processing of the uniprot-proteome-.nt files for 2.7. I noticed the size of many of the nt files has decreased from the 2.6 release.
According to the …
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Dear professor:
I cannot find this txt file "seurat_clust_1620.txt" in example 3 "Run STitch3D on the Drosophila embryo dataset"
clust = pd.read_csv("./data/Calderon_2022/seurat_clust_1620.txt", sep…