databio/bedbase issues and pull requests

#83 - Following BEDbase releases

Issue - State: closed - Opened by jwokaty about 1 month ago - 3 comments

#82 - bedms tutorial

Pull Request - State: open - Opened by saanikat about 1 month ago

#81 - bedms tutorial

Pull Request - State: closed - Opened by saanikat about 1 month ago

#80 - Storing of 2 same bed files with different columns

Issue - State: open - Opened by khoroshevskyi about 1 month ago
Labels: brainstorming

#79 - File changed from bed3+0 to bed6+4?

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

#78 - Remove old search doc branch

Pull Request - State: closed - Opened by ClaudeHu about 2 months ago

#77 - added creation of the graph of geo bed files

Pull Request - State: closed - Opened by khoroshevskyi 2 months ago

#76 - Search doc update

Pull Request - State: closed - Opened by ClaudeHu 5 months ago

#75 - Dev search docs

Pull Request - State: closed - Opened by khoroshevskyi 6 months ago

#75 - Dev search docs

Pull Request - State: closed - Opened by khoroshevskyi 6 months ago

#74 - Geniml Release

Pull Request - State: closed - Opened by khoroshevskyi 6 months ago

#74 - Geniml Release

Pull Request - State: closed - Opened by khoroshevskyi 6 months ago

#73 - 2024-05 BEDbase sprint

Issue - State: closed - Opened by nsheff 6 months ago - 1 comment

#71 - Update tokenizer docs

Pull Request - State: closed - Opened by nleroy917 6 months ago

#71 - Update tokenizer docs

Pull Request - State: closed - Opened by nleroy917 6 months ago

#70 - updated bedhost docs

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

#70 - updated bedhost docs

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

#69 - Universes in the database

Issue - State: closed - Opened by khoroshevskyi 7 months ago - 2 comments
Labels: solved

#68 - Updated bedbase docs

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

#68 - Updated bedbase docs

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

#67 - Data curation

Issue - State: open - Opened by khoroshevskyi 7 months ago - 3 comments
Labels: priority-high, DATA

#67 - Data curation

Issue - State: open - Opened by khoroshevskyi 7 months ago - 3 comments
Labels: priority-high, DATA

#66 - Update document according to changes in geniml.search

Pull Request - State: closed - Opened by ClaudeHu 8 months ago

#66 - Update document according to changes in geniml.search

Pull Request - State: closed - Opened by ClaudeHu 8 months ago

#65 - Dev julia

Pull Request - State: closed - Opened by nsheff 8 months ago

#65 - Dev julia

Pull Request - State: closed - Opened by nsheff 8 months ago

#64 - bedset/genomes returns 500 error

Issue - State: closed - Opened by jwokaty 8 months ago - 1 comment
Labels: likely-solved

#64 - bedset/genomes returns 500 error

Issue - State: closed - Opened by jwokaty 8 months ago - 1 comment
Labels: likely-solved

#63 - BEDbase documentation updates

Issue - State: closed - Opened by nsheff 8 months ago - 1 comment
Labels: DOCS

#63 - BEDbase documentation updates

Issue - State: closed - Opened by nsheff 8 months ago - 1 comment
Labels: DOCS

#62 - 2024-03 BEDbase sprint

Issue - State: closed - Opened by nsheff 8 months ago - 1 comment
Labels: meta-issue

#61 - Bad gateway for api.bedbase.org

Issue - State: closed - Opened by jwokaty 8 months ago - 2 comments

#61 - Bad gateway for api.bedbase.org

Issue - State: closed - Opened by jwokaty 8 months ago - 2 comments

#60 - Added bedboss and bedhost and bbconf docs

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#60 - Added bedboss and bedhost and bbconf docs

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#59 - text2bednn doc update

Pull Request - State: closed - Opened by ClaudeHu 9 months ago

#59 - text2bednn doc update

Pull Request - State: closed - Opened by ClaudeHu 9 months ago

#58 - Bedboss

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#58 - Bedboss

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#57 - Copy over fresh docs

Pull Request - State: closed - Opened by nleroy917 9 months ago

#57 - Copy over fresh docs

Pull Request - State: closed - Opened by nleroy917 9 months ago

#56 - Streamline retrieving pephub metadata of bed records

Issue - State: closed - Opened by nsheff 11 months ago - 4 comments
Labels: priority-high, likely-solved

#56 - Streamline retrieving pephub metadata of bed records

Issue - State: closed - Opened by nsheff 11 months ago - 4 comments
Labels: priority-high, likely-solved

#54 - Identifying extra columns in BED files

Issue - State: closed - Opened by jwokaty 11 months ago - 6 comments
Labels: question

#53 - Make GEO uploading automatic by using bbuploader

Issue - State: closed - Opened by khoroshevskyi 12 months ago - 1 comment

#52 - Add Encode dataset to bedbase

Issue - State: closed - Opened by khoroshevskyi 12 months ago - 2 comments
Labels: priority-high

#52 - Add Encode dataset to bedbase

Issue - State: closed - Opened by khoroshevskyi 12 months ago - 2 comments
Labels: priority-high

#51 - Add LOLA dataset to bedbase

Issue - State: closed - Opened by khoroshevskyi 12 months ago - 4 comments
Labels: priority-high

#51 - Add LOLA dataset to bedbase

Issue - State: closed - Opened by khoroshevskyi 12 months ago - 4 comments
Labels: priority-high

#49 - Streamlining bedboss running

Issue - State: closed - Opened by nsheff about 1 year ago
Labels: likely-solved, meta-issue

#49 - Streamlining bedboss running

Issue - State: closed - Opened by nsheff about 1 year ago
Labels: likely-solved, meta-issue

#48 - Dev bedboss

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

#48 - Dev bedboss

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

#47 - Dev

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

#46 - Reconfigured deployment to divide front and back-end

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

#46 - Reconfigured deployment to divide front and back-end

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

#45 - Bedbase --> next steps in details (backend)

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

#45 - Bedbase --> next steps in details (backend)

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

#41 - Index all BED files into vector database

Issue - State: closed - Opened by nsheff over 1 year ago - 6 comments
Labels: likely-solved

#41 - Index all BED files into vector database

Issue - State: closed - Opened by nsheff over 1 year ago - 6 comments
Labels: likely-solved

#37 - BEDbase natural language search data table for embedding approach

Issue - State: open - Opened by nsheff over 1 year ago - 11 comments

#36 - Bedstats: should allowed database update if data changed for a bedfile

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 1 comment
Labels: enhancement

#36 - Bedstats: should allowed database update if data changed for a bedfile

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 1 comment
Labels: enhancement

#34 - Bedboss/Bedstats: how to get required files needed for Bedstats (GD)

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago

#34 - Bedboss/Bedstats: how to get required files needed for Bedstats (GD)

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago

#32 - Pipestat/bbconf

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 3 comments

#32 - Pipestat/bbconf

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 3 comments

#31 - Bedembed/human-friendly search: need to be useful not just a proof of concept

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 1 comment
Labels: enhancement, priority-high

#31 - Bedembed/human-friendly search: need to be useful not just a proof of concept

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 1 comment
Labels: enhancement, priority-high

#30 - automate BEDbase data process pipeline (heavy processing)

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 2 comments
Labels: enhancement

#30 - automate BEDbase data process pipeline (heavy processing)

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 2 comments
Labels: enhancement

#29 - Bedhost-ui: ui upgrade

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago
Labels: enhancement, likely-solved

#29 - Bedhost-ui: ui upgrade

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago
Labels: enhancement, likely-solved

#28 - Bedstats: resolving failed GD stats/plot for genomes other than hg19/hg38/mm10

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago
Labels: likely-solved

#28 - Bedstats: resolving failed GD stats/plot for genomes other than hg19/hg38/mm10

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago
Labels: likely-solved

#27 - Bedqc: bedboss should automatically ignore bedqc-filtered BED files

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 2 comments
Labels: likely-solved

#27 - Bedqc: bedboss should automatically ignore bedqc-filtered BED files

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 2 comments
Labels: likely-solved

#26 - Bedmaker: fail to generate bigbed files

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 1 comment
Labels: bug, likely-solved

#26 - Bedmaker: fail to generate bigbed files

Issue - State: closed - Opened by xuebingjie1990 almost 2 years ago - 1 comment
Labels: bug, likely-solved

#25 - Flexibility of back-end data

Issue - State: closed - Opened by nsheff about 2 years ago - 2 comments
Labels: enhancement

#25 - Flexibility of back-end data

Issue - State: closed - Opened by nsheff about 2 years ago - 2 comments
Labels: enhancement

#24 - Bedboss: testing with bedboss

Issue - State: closed - Opened by xuebingjie1990 about 2 years ago - 8 comments

#24 - Bedboss: testing with bedboss

Issue - State: closed - Opened by xuebingjie1990 about 2 years ago - 8 comments

#23 - Bedbuncher/Bedhost-ui: How to organize/show BED sets with different ref genome on BEDbase.org

Issue - State: closed - Opened by xuebingjie1990 about 2 years ago - 1 comment
Labels: brainstorming

#23 - Bedbuncher/Bedhost-ui: How to organize/show BED sets with different ref genome on BEDbase.org

Issue - State: closed - Opened by xuebingjie1990 about 2 years ago - 1 comment
Labels: brainstorming

#21 - Update info about downloading all bed files

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

#21 - Update info about downloading all bed files

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

#20 - Link BEDbase with pephub: use PEPhub for auto metadata update

Issue - State: closed - Opened by xuebingjie1990 almost 3 years ago - 1 comment
Labels: brainstorming

#20 - Link BEDbase with pephub: use PEPhub for auto metadata update

Issue - State: closed - Opened by xuebingjie1990 almost 3 years ago - 1 comment
Labels: brainstorming

#19 - Solved issues of non existing variables

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

#19 - Solved issues of non existing variables

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

#18 - Environment variable $CODE is not initialized

Issue - State: closed - Opened by khoroshevskyi almost 3 years ago - 1 comment

#18 - Environment variable $CODE is not initialized

Issue - State: closed - Opened by khoroshevskyi almost 3 years ago - 1 comment

#17 - environment variable $REFGENIE is not added in the tutorial

Issue - State: closed - Opened by khoroshevskyi almost 3 years ago - 1 comment

#17 - environment variable $REFGENIE is not added in the tutorial

Issue - State: closed - Opened by khoroshevskyi almost 3 years ago - 1 comment

GitHub / databio/bedbase issues and pull requests