Comments (3)
nsheff
commented on June 25, 2024
In the most recent version, readBed should accept anything that is not + or - and consider that unknown -- so * or . should be the same. have you tried the latest version from github (which hasn't been put into bioconductor yet)? I think it should work...
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imk1
commented on June 25, 2024
I was using the version in bioconductor. Thanks for the suggestion!
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nsheff
commented on June 25, 2024
Just letting you know, I've pushed this change now into the dev version of bioconductor (it should build in a few days).
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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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