Ecosyste.ms: Issues

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GitHub / nsheff/lola issues and pull requests

#47 - Database download from "latest databases" doesnt work - 403 Forbidden Error

Issue - State: closed - Opened by sreichl 6 months ago - 3 comments

#46 - Error when trying to load a regionDB

Issue - State: open - Opened by HanneHjorthaug over 1 year ago

#45 - Fisher test - two sided hypothesis

Issue - State: open - Opened by JBinkowski almost 2 years ago

#44 - Error by using extractEnrichmentOverlap function

Issue - State: closed - Opened by thwagner0815 about 2 years ago

#43 - P4 tool not grouping according to the paper!!

Issue - State: open - Opened by 09Raghu09 over 2 years ago

#42 - LOLA runLOLA-regionDB to use for tissue-specific TFBS

Issue - State: open - Opened by shanie-landen over 3 years ago

#41 - R package error

Issue - State: open - Opened by yangyongsan-bio over 3 years ago - 4 comments

#40 - Each of the 2 combined objects has sequence levels not in the other:

Issue - State: closed - Opened by storytc almost 4 years ago - 4 comments

#38 - Error if GRangesList has names

Issue - State: open - Opened by j-lawson over 4 years ago - 2 comments

#37 - iGD integration

Pull Request - State: open - Opened by joseverdezoto over 4 years ago

#36 - testing for enrichment of significant individual cpgs

Issue - State: open - Opened by lxw391 almost 5 years ago - 2 comments

#35 - PEP loading function for LOLA

Pull Request - State: open - Opened by joseverdezoto almost 5 years ago - 4 comments

#34 - PEP tag system

Issue - State: open - Opened by nsheff about 5 years ago
Labels: enhancement

#33 - Can't load an example regionDB.

Issue - State: open - Opened by lining-yuan about 5 years ago - 3 comments

#32 - PEP file read caching

Issue - State: open - Opened by nsheff about 5 years ago - 2 comments

#31 - runLOLA results table for PEP databases

Issue - State: open - Opened by joseverdezoto about 5 years ago

#30 - Fix typo, add link to other vignette

Pull Request - State: closed - Opened by j-lawson over 5 years ago

#29 - cistrome_mm10

Issue - State: open - Opened by byerscan almost 6 years ago - 2 comments

#28 - Inclusion of mm10 JASAPR prediction track into LOLA JASPAR

Issue - State: open - Opened by holgerbrandl about 6 years ago - 3 comments

#27 - Different results between LOLAweb interactive server and local R package

Issue - State: open - Opened by NyxSLY over 6 years ago - 7 comments

#26 - Re-order result columns

Issue - State: open - Opened by nsheff over 6 years ago

#25 - Add in missing cellType/antibody entries for encodeTFBSmm10

Issue - State: closed - Opened by oneillkza about 7 years ago - 6 comments

#24 - hg38 database

Issue - State: closed - Opened by sb5169 about 7 years ago - 1 comment

#23 - OddsRatio or logOddsRatio ?

Issue - State: closed - Opened by gouthamatla about 7 years ago - 2 comments
Labels: question

#22 - The readBed function does not transform from 0-based to 1-based coordinates

Issue - State: closed - Opened by deyanyosifov about 7 years ago - 4 comments

#21 - specify data.table's melt

Pull Request - State: closed - Opened by nsheff over 7 years ago

#20 - two-sided fisher test

Issue - State: closed - Opened by bmreilly over 7 years ago - 1 comment

#19 - readBed Input Format

Issue - State: closed - Opened by imk1 over 7 years ago - 3 comments

#18 - Merging database region-sets

Issue - State: open - Opened by flopflip over 7 years ago - 2 comments

#16 - Make refreshSizes an option in readRegionSetAnnotation

Issue - State: closed - Opened by JonBarenboim over 7 years ago - 1 comment

#15 - 0-based bed files in database are not properly translated to 1-based regions for LOLA

Issue - State: closed - Opened by ktrns almost 8 years ago - 8 comments

#14 - readBed is not consistent with import.bed

Issue - State: closed - Opened by wcstcyx almost 8 years ago - 1 comment

#13 - Combining LOLA Core and Extended

Issue - State: closed - Opened by rajitz over 8 years ago - 1 comment

#12 - Histone marks collections

Issue - State: open - Opened by enricoferrero over 8 years ago

#10 - Can't load LOLAExt with loadRegionDB()

Issue - State: closed - Opened by enricoferrero over 8 years ago - 4 comments

#9 - Add a Gitter chat badge to README.md

Pull Request - State: closed - Opened by gitter-badger over 9 years ago

#8 - Command line interface

Issue - State: open - Opened by ghost over 9 years ago

#7 - No error on bad regionDB

Issue - State: closed - Opened by nsheff over 9 years ago

#6 - Clarifications

Pull Request - State: closed - Opened by fhalbritter over 9 years ago - 3 comments

#5 - Column naming

Issue - State: closed - Opened by fhalbritter over 9 years ago - 3 comments

#4 - gettingStarted.Rmd

Issue - State: closed - Opened by fhalbritter over 9 years ago - 2 comments

#3 - clarify checkUniverseAppropriateness

Issue - State: open - Opened by nsheff over 9 years ago

#2 - simpleCache dependency

Issue - State: closed - Opened by nsheff over 9 years ago
Labels: enhancement

#1 - reading zipped bed files

Issue - State: open - Opened by nsheff almost 10 years ago - 1 comment