Comments (4)
enricoferrero
commented on July 24, 2024
To fix this it is sufficient to include a collection.txt file in roadmap_epigenomics and jaspar_motifs similar to those used in LOLACore (e.g.: I modified the one from encode_tfbs).
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nsheff
commented on July 24, 2024
Thanks for reporting this; I haven't had time to confirm but it should be an easy fix. I'll keep you posted...
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nsheff
commented on July 24, 2024
I finally fixed this in the released version; I also fixed a bug in the motif calculation that made the jaspar collection bad. Please update to the latest LOLAExt.
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nsheff
commented on July 24, 2024
(you can download the latest databases here: http://databio.org/regiondb)
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Related Issues (20)
- hg38 database HOT 1
- Add in missing cellType/antibody entries for encodeTFBSmm10 HOT 6
- Re-order result columns
- Different results between LOLAweb interactive server and local R package HOT 7
- Inclusion of mm10 JASAPR prediction track into LOLA JASPAR HOT 3
- cistrome_mm10 HOT 2
- runLOLA results table for PEP databases
- PEP file read caching HOT 2
- Can't load an example regionDB. HOT 3
- PEP tag system
- testing for enrichment of significant individual cpgs HOT 2
- Error if GRangesList has names HOT 2
- question: how to test two region sets for differential enrichment with buildRestrictedUniverse? HOT 2
- Each of the 2 combined objects has sequence levels not in the other: HOT 4
- R package error HOT 4
- LOLA runLOLA-regionDB to use for tissue-specific TFBS
- P4 tool not grouping according to the paper!!
- Error by using extractEnrichmentOverlap function
- Fisher test - two sided hypothesis
- Error when trying to load a regionDB
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