waldronlab/bugsigdbr issues and pull requests

#62 - Update default import to Zenodo release v1.2.2

Pull Request - State: closed - Opened by jwokaty 4 months ago

#61 - Make release

Issue - State: closed - Opened by jwokaty 4 months ago - 22 comments

#60 - Error when using all ranks and the exact.level argument is FALSE in getSignatures

Issue - State: closed - Opened by sdgamboa 4 months ago - 4 comments
Labels: bug

#59 - Modified unit test for differences

Pull Request - State: closed - Opened by cmirzayi 5 months ago - 2 comments

#58 - Create a unit test for the size of the bugsigdb export

Issue - State: closed - Opened by cmirzayi 5 months ago - 2 comments

#57 - Default if importBugSigDB does no import the latest Zenodo stable version

Issue - State: closed - Opened by sdgamboa about 1 year ago - 3 comments

#56 - fix min.size; apply unique first

Pull Request - State: closed - Opened by LiNk-NY about 1 year ago - 1 comment

#55 - Use BugSigDbExports v1.2.0

Pull Request - State: closed - Opened by jwokaty about 1 year ago

#54 - [BUG] getSignatures can produce signatures < min.size

Issue - State: closed - Opened by jwokaty about 1 year ago - 1 comment

#53 - `importBugSigDB` function returns error

Issue - State: closed - Opened by npechl about 1 year ago - 3 comments

#52 - Error if more than 1 devel cache

Issue - State: open - Opened by jwokaty about 1 year ago

#51 - add bugsigdb-related links

Pull Request - State: closed - Opened by lwaldron over 1 year ago

#49 - Release 3.18

Issue - State: closed - Opened by lwaldron over 1 year ago - 52 comments
Labels: minor version

#48 - pass arguments from writeGMT to cat

Pull Request - State: closed - Opened by lwaldron over 1 year ago - 1 comment

#47 - GitHub Action Error

Issue - State: closed - Opened by jwokaty over 1 year ago - 2 comments

#46 - Remove reference to main

Pull Request - State: closed - Opened by jwokaty over 1 year ago

#45 - Can't download uberon

Issue - State: closed - Opened by sdgamboa over 1 year ago - 4 comments

#44 - subsetByOntology: include query term itself

Issue - State: closed - Opened by cmirzayi over 1 year ago - 6 comments
Labels: enhancement

#43 - [BUG] Study 722 is missing k__bacteria from MetaPhlAn taxon names

Issue - State: closed - Opened by cmirzayi almost 2 years ago - 1 comment

#42 - Can't create signatures

Issue - State: closed - Opened by sdgamboa almost 2 years ago - 7 comments
Labels: bug

#41 - version should accept full SHA

Issue - State: closed - Opened by lwaldron almost 2 years ago - 1 comment
Labels: enhancement

#40 - Unexpected output format when creating signatures for study 727

Issue - State: closed - Opened by sdgamboa almost 2 years ago - 1 comment
Labels: bug

#39 - documentation enhancement of using devel

Issue - State: closed - Opened by lgeistlinger almost 2 years ago - 1 comment
Labels: documentation

#38 - import PMID column as numeric

Issue - State: closed - Opened by lwaldron almost 2 years ago - 3 comments

#37 - importBugSigDB(version = 'devel', cache = FALSE) not reading Study 727

Issue - State: closed - Opened by sdgamboa almost 2 years ago - 16 comments

#35 - standard enrichment workflow

Issue - State: open - Opened by lwaldron about 2 years ago - 2 comments
Labels: documentation

#34 - 3.16 Release?

Issue - State: closed - Opened by jwokaty over 2 years ago - 1 comment

#33 - Fix GitHub actions

Pull Request - State: closed - Opened by jwokaty over 2 years ago

#32 - Warning in importBugSigDB() when updating a previously cached version (windows-only)

Issue - State: closed - Opened by cmirzayi over 2 years ago - 3 comments
Labels: bug

#31 - Update default importBugSigDB to v1.1.0

Pull Request - State: closed - Opened by jwokaty almost 3 years ago - 3 comments

#30 - BugSigDB 1.1.0 release (for Bioconductor 3.15)

Issue - State: closed - Opened by jwokaty almost 3 years ago - 3 comments

#29 - all(grepl("^[A-Z][a-z ]+$", names(s))) is not TRUE

Issue - State: closed - Opened by lwaldron almost 3 years ago - 2 comments

#28 - importBugSigDB mixing Experiments?

Issue - State: closed - Opened by lwaldron almost 3 years ago - 4 comments
Labels: bug

#27 - importBugSigDB(version="devel") is missing studies

Issue - State: closed - Opened by cmirzayi about 3 years ago - 2 comments
Labels: bug

#26 - Issues in recent build report

Issue - State: closed - Opened by lgeistlinger about 3 years ago - 1 comment

#25 - Correct version

Pull Request - State: closed - Opened by jwokaty about 3 years ago

#24 - Update Github actions

Issue - State: closed - Opened by jwokaty about 3 years ago - 4 comments

#23 - Add version argument

Pull Request - State: closed - Opened by jwokaty about 3 years ago - 4 comments

#22 - Using cache might report using a cached copy from future date?

Issue - State: open - Opened by jwokaty about 3 years ago - 1 comment

#21 - Informative news for 1.0.0

Pull Request - State: closed - Opened by lwaldron over 3 years ago - 2 comments

#20 - Pull from stable/zenodo

Issue - State: closed - Opened by jwokaty over 3 years ago - 12 comments
Labels: enhancement

#19 - Pulling from github causes BiocCheck error

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

#18 - Update version in DESCRIPTION

Pull Request - State: closed - Opened by jwokaty over 3 years ago

#17 - Remove dump_release.R

Pull Request - State: closed - Opened by jwokaty over 3 years ago

#16 - Improve formatting

Pull Request - State: closed - Opened by jwokaty over 3 years ago - 1 comment

#15 - Address recommendations from Bioconductor

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

#14 - Update check-bioc.yml bioc to 3.14

Pull Request - State: closed - Opened by jwokaty over 3 years ago

#13 - ontology-based queries for experimental factors and body sites

Issue - State: closed - Opened by lgeistlinger over 3 years ago - 1 comment
Labels: enhancement

#11 - Scrape export links from export page

Issue - State: closed - Opened by lgeistlinger over 3 years ago - 1 comment

#10 - [BUG] GHA fails on mac and windows container due to BiocVersion issue

Issue - State: closed - Opened by lgeistlinger over 3 years ago - 1 comment

#9 - endomorphic version of of getSignatures `tax.level` argument

Issue - State: closed - Opened by lwaldron over 3 years ago - 6 comments
Labels: enhancement

#8 - Change email

Pull Request - State: closed - Opened by jwokaty over 3 years ago

#7 - Prepare for submission

Pull Request - State: closed - Opened by jwokaty over 3 years ago

#6 - Bioc submission

Issue - State: closed - Opened by lgeistlinger over 3 years ago - 8 comments

#5 - Calc pairwise overlaps

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

#4 - Create package with pkgdown GH pages

Pull Request - State: closed - Opened by jwokaty almost 4 years ago - 2 comments

#3 - Create shell R package + pkgdown gh-pages site

Issue - State: closed - Opened by lwaldron almost 4 years ago

#2 - Add importBugSigDB to R package

Issue - State: closed - Opened by lwaldron almost 4 years ago - 7 comments

#1 - add writeGMT function to R package

Issue - State: closed - Opened by lwaldron almost 4 years ago - 1 comment

GitHub / waldronlab/bugsigdbr issues and pull requests