warelab/gramene-mongodb issues and pull requests

#76 - index for location query (map, region, start, end)

Pull Request - State: closed - Opened by ajo2995 7 months ago

#75 - sorghum_v7

Pull Request - State: closed - Opened by ajo2995 11 months ago

#74 - grapevine_v4

Pull Request - State: closed - Opened by ajo2995 almost 1 year ago

#73 - Main68

Pull Request - State: closed - Opened by ajo2995 about 1 year ago

#72 - Oryza v7

Pull Request - State: closed - Opened by ajo2995 over 1 year ago

#71 - Sorghum v6

Pull Request - State: closed - Opened by ajo2995 over 1 year ago

#70 - Oryza v3 rerun

Pull Request - State: closed - Opened by ajo2995 almost 3 years ago

#69 - Rice pangenome3

Pull Request - State: closed - Opened by ajo2995 almost 3 years ago

#68 - updates for sorghum_v2

Pull Request - State: closed - Opened by ajo2995 over 3 years ago

#67 - Bump mongodb from 2.2.36 to 3.6.1

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#66 - Panther protein classifications

Issue - State: open - Opened by ajo2995 almost 6 years ago

#65 - review gene tree internal node annotation code

Issue - State: open - Opened by ajo2995 almost 6 years ago

#64 - Release59

Pull Request - State: closed - Opened by ajo2995 about 6 years ago

#63 - flatten tree in db

Issue - State: open - Opened by ajo2995 about 7 years ago - 2 comments
Labels: enhancement

#62 - collect the taxon ids of duplication nodes

Pull Request - State: closed - Opened by ajo2995 over 7 years ago

#61 - Reactome api update

Pull Request - State: closed - Opened by ajo2995 over 7 years ago

#60 - Release55

Pull Request - State: closed - Opened by ajo2995 over 7 years ago

#59 - associate duplication nodes to genes

Issue - State: open - Opened by ajo2995 over 7 years ago

#58 - update taxon_id in gene trees for subspecies

Issue - State: open - Opened by ajo2995 over 7 years ago

#57 - add display_name to maps collection

Issue - State: open - Opened by ajo2995 over 7 years ago

#56 - Release52

Pull Request - State: closed - Opened by ajo2995 almost 8 years ago

#55 - Dev

Pull Request - State: closed - Opened by ajo2995 over 8 years ago

#54 - Release51

Pull Request - State: closed - Opened by ajo2995 over 8 years ago

#53 - Evidence code

Pull Request - State: closed - Opened by ajo2995 over 8 years ago

#52 - Proposal: Refactor taxon/location information.

Issue - State: open - Opened by mycrobe over 8 years ago
Labels: enhancement, analysis

#51 - Add exon boundaries to gene tree

Issue - State: closed - Opened by ajo2995 almost 9 years ago

#50 - GO/PO evidence codes fixes #48

Pull Request - State: closed - Opened by ajo2995 almost 9 years ago

#49 - ancestors fields should only be in solr docs

Issue - State: closed - Opened by ajo2995 almost 9 years ago

#48 - add GO/PO evidence codes to genes docs

Issue - State: closed - Opened by ajo2995 almost 9 years ago

#47 - bring in cyc pathways

Issue - State: open - Opened by ajo2995 almost 9 years ago
Labels: enhancement, analysis

#46 - many homologs are missing in v50 genes

Issue - State: closed - Opened by ajo2995 almost 9 years ago
Labels: bug

#45 - Taxonomy subsets

Pull Request - State: closed - Opened by ajo2995 almost 9 years ago

#44 - Get species tree and taxonomy from compara

Pull Request - State: closed - Opened by ajo2995 almost 9 years ago

#43 - Non zm4 changes

Pull Request - State: closed - Opened by ajo2995 almost 9 years ago

#43 - Non zm4 changes

Pull Request - State: closed - Opened by ajo2995 almost 9 years ago

#42 - Use compara as source for species taxonomy information

Issue - State: closed - Opened by mycrobe almost 9 years ago - 3 comments
Labels: enhancement, analysis

#41 - No simple way to map system_name to species name

Issue - State: closed - Opened by mycrobe almost 9 years ago - 1 comment
Labels: enhancement

#40 - tweak representative gene scoring

Issue - State: closed - Opened by ajo2995 almost 9 years ago

#39 - Get Curator Summaries from AraPort.

Issue - State: closed - Opened by mycrobe almost 9 years ago - 2 comments
Labels: enhancement, araport

#38 - import TAIR curator summaries

Issue - State: closed - Opened by ajo2995 almost 9 years ago - 1 comment

#38 - import TAIR curator summaries

Issue - State: closed - Opened by ajo2995 almost 9 years ago - 1 comment

#37 - remove empty homology fields

Issue - State: closed - Opened by ajo2995 almost 9 years ago - 1 comment
Labels: bug

#36 - Update homology document

Issue - State: closed - Opened by mycrobe almost 9 years ago - 3 comments
Labels: bug

#36 - Update homology document

Issue - State: closed - Opened by mycrobe almost 9 years ago - 3 comments
Labels: bug

#35 - TCM_006793 does not have domain root specified.

Issue - State: closed - Opened by mycrobe almost 9 years ago - 1 comment
Labels: bug

#34 - Arrayify

Pull Request - State: closed - Opened by ajo2995 almost 9 years ago

#34 - Arrayify

Pull Request - State: closed - Opened by ajo2995 almost 9 years ago

#33 - Investigate using bagpipes for automation

Issue - State: open - Opened by mycrobe almost 9 years ago
Labels: analysis

#32 - Rename indexCommands.js

Issue - State: closed - Opened by mycrobe almost 9 years ago
Labels: bug

#32 - Rename indexCommands.js

Issue - State: closed - Opened by mycrobe almost 9 years ago
Labels: bug

#31 - Exons and Transcripts should be in an array instead of an object

Issue - State: closed - Opened by mycrobe almost 9 years ago - 5 comments
Labels: enhancement

#31 - Exons and Transcripts should be in an array instead of an object

Issue - State: closed - Opened by mycrobe almost 9 years ago - 5 comments
Labels: enhancement

#30 - Taxonomy core should include full NCBI taxonomy

Issue - State: closed - Opened by mycrobe almost 9 years ago - 1 comment
Labels: enhancement

#29 - ontology alt_id entries are missing

Issue - State: closed - Opened by ajo2995 almost 9 years ago

#29 - ontology alt_id entries are missing

Issue - State: closed - Opened by ajo2995 almost 9 years ago

#28 - add overlapping dna_align_feature labels to genes

Issue - State: open - Opened by ajo2995 almost 9 years ago - 2 comments

#28 - add overlapping dna_align_feature labels to genes

Issue - State: open - Opened by ajo2995 almost 9 years ago - 2 comments

#27 - add id_history field

Issue - State: open - Opened by ajo2995 almost 9 years ago - 3 comments
Labels: enhancement

#26 - combine core and otherfeatures gene models

Issue - State: open - Opened by ajo2995 almost 9 years ago - 1 comment

#25 - Genes in genetree documents do not have species name

Issue - State: closed - Opened by mycrobe almost 9 years ago - 4 comments
Labels: bug