nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges

http://code.databio.org/LOLA

nsheff/LOLA Issues

Error when trying to load a regionDB
Updated a year ago
Fisher test - two sided hypothesis
Updated 2 years ago
Error by using extractEnrichmentOverlap function
Closed 2 years ago
R package error
Updated 2 years ago4
P4 tool not grouping according to the paper!!
Updated 2 years ago
LOLA runLOLA-regionDB to use for tissue-specific TFBS
Updated 3 years ago
Each of the 2 combined objects has sequence levels not in the other:
Closed 4 years ago4
question: how to test two region sets for differential enrichment with buildRestrictedUniverse?
Updated 4 years ago2
Error if GRangesList has names
Updated 4 years ago2
testing for enrichment of significant individual cpgs
Updated 5 years ago2
Can't load an example regionDB.
Updated 5 years ago3
PEP tag system
Updated 5 years ago
PEP file read caching
Updated 5 years ago2
runLOLA results table for PEP databases
Updated 5 years ago
cistrome_mm10
Updated 6 years ago2
Inclusion of mm10 JASAPR prediction track into LOLA JASPAR
Updated 6 years ago3
Different results between LOLAweb interactive server and local R package
Updated 6 years ago7
Re-order result columns
Updated 6 years ago
Add in missing cellType/antibody entries for encodeTFBSmm10
Closed 6 years ago6
OddsRatio or logOddsRatio ?
Closed 7 years ago2
hg38 database
Closed 7 years ago1
The readBed function does not transform from 0-based to 1-based coordinates
Closed 7 years ago4
readBed Input Format
Closed 7 years ago3
Make refreshSizes an option in readRegionSetAnnotation
Closed 7 years ago1
two-sided fisher test
Closed 7 years ago1
Merging database region-sets
Updated 7 years ago2
Error in setnames(scoreTable, c("Var1", "Var2", "value"), c("userSet", : Items of 'old' not found in column names: Var1,Var2
Closed 7 years ago3
Can't load LOLAExt with loadRegionDB()
Closed 8 years ago4
0-based bed files in database are not properly translated to 1-based regions for LOLA
Closed 8 years ago8
readBed is not consistent with import.bed
Closed 8 years ago1
Combining LOLA Core and Extended
Closed 8 years ago1
Histone marks collections
Updated 8 years ago
Negative c entry in table. Bug with userSetsLength; this should not happen.
Updated 8 years ago9
reading zipped bed files
Updated 8 years ago1
gettingStarted.Rmd
Closed 9 years ago2
No error on bad regionDB
Closed 9 years ago
Command line interface
Updated 9 years ago
Column naming
Closed 9 years ago3
simpleCache dependency
Closed 9 years ago
clarify checkUniverseAppropriateness
Updated 9 years ago