leoisl/plasnet issues and pull requests

#64 - sparsely connected components in the network

Issue - State: open - Opened by iwangtoknow about 2 months ago

#63 - officially_new_plasnet

Pull Request - State: closed - Opened by Zhuo-DIAO 6 months ago

#62 - chore(main): release 0.6.0

Pull Request - State: closed - Opened by leoisl 6 months ago - 1 comment
Labels: autorelease: tagged

#61 - Switch to unweighted classification

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

#60 - fix: mark with stars the nodes we actually use in clustering as hubs

Issue - State: open - Opened by leoisl 6 months ago

#59 - Optionally output cytoscape json files

Pull Request - State: closed - Opened by babayagaofficial 8 months ago - 1 comment

#58 - chore(main): release 0.5.1

Pull Request - State: closed - Opened by leoisl 12 months ago - 1 comment
Labels: autorelease: tagged

#57 - fix: fix bug: key error exception when building RH PLSDB DB

Pull Request - State: closed - Opened by leoisl 12 months ago

#56 - bug: key error exception when building RH PLSDB DB

Issue - State: closed - Opened by leoisl 12 months ago

#55 - Second iteration hub plasmids not marked in visualisation

Issue - State: open - Opened by babayagaofficial almost 1 year ago - 3 comments

#54 - chore(main): release 0.5.0

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#53 - feat: now creating a hub_plasmids.csv file when running the plasnet type command explicitly listing each hub plasmid

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

#52 - chore(main): release 0.4.2

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#51 - refactor: switching terminology from blackhole to hub

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

#50 - chore(main): release 0.4.1

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#49 - fix: adds param use_cached to BlackholeGraph._get_blackhole_plasmids(), solving the slowdown introduced in releases v0.3.3 and v0.3.4

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

#48 - Switch terminology from blackhole to hub

Issue - State: closed - Opened by leoisl about 1 year ago

#47 - Create a blackholes.csv file in the output explicitly denoting each blackhole in each community

Issue - State: closed - Opened by leoisl about 1 year ago

#46 - chore(main): release 0.4.0

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#45 - chore(main): release 0.4.0

Pull Request - State: closed - Opened by leoisl about 1 year ago
Labels: autorelease: pending

#44 - ci: updating the messages in release please changelog

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

#43 - chore(main): release 0.4.0

Pull Request - State: closed - Opened by leoisl about 1 year ago
Labels: autorelease: pending

#42 - feat: now we can provide metadata to plasmids (param --plasmids-metadata in plasnet split)

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

#41 - Recent changes (v0.3.3 and v0.3.4) might have made plasnet slow for very large graphs

Issue - State: closed - Opened by leoisl about 1 year ago - 2 comments
Labels: high priority

#40 - Make --add-sample-hits subcommand accept communities

Issue - State: open - Opened by leoisl about 1 year ago
Labels: high priority

#39 - chore(main): release 0.3.4

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#38 - fix: iteratively removing blackholes until convergence

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

#37 - chore(main): release 0.3.3

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#36 - fix: fix a bug where plasnet was not correctly recognising blackholes in type command

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

#35 - chore(main): release 0.3.2

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#34 - fix: now setting the default colour for blackhole plasmids instead of erroring out with KeyError

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

#33 - chore(main): release 0.3.1

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#32 - ci: re-enabling python versions 3.8, 3.9 and 3.10 in the CI tests

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

#31 - chore(main): release 0.3.1

Pull Request - State: closed - Opened by leoisl about 1 year ago
Labels: autorelease: pending

#30 - docs: small fix to the link of add-sample-hits output in README.md

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

#29 - chore(main): release 0.3.0

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#28 - feat: add sample hits subcommand

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

#27 - chore(main): release 0.2.1

Pull Request - State: closed - Opened by leoisl about 1 year ago
Labels: autorelease: pending

#26 - refactor: Visualisation refactor

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

#25 - ACT images on the edges

Issue - State: open - Opened by leoisl about 1 year ago
Labels: fix later

#24 - Add number of genes, number of hit genes to visualisation

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

#23 - Add hit proportion filter

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

#22 - Add bottom table with metadata/data about selected nodes

Issue - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: high priority

#21 - Avoid using same colours for different neighbouring typings

Issue - State: open - Opened by leoisl about 1 year ago
Labels: low priority

#20 - chore(main): release 0.2.0

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#19 - New feature: edges now show the split and type distance in their labels and other bug fixes

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

#18 - chore(main): release 0.1.7

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: autorelease: tagged

#17 - ci: now correctly making release-pypi deploy to pypi once a release is published

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

#16 - chore(main): release 0.1.6

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#15 - ci: allowing release-pypi workflow to be manually triggered

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

#14 - chore(main): release 0.1.5

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#13 - ci: running release-pypi when release is published

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

#12 - chore(main): release 0.1.4

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#11 - ci: release-pypi now triggered when a release is created

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

#10 - chore(main): release 0.1.3

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#9 - ci: fixing gh-pages upload

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

#8 - chore(main): release 0.1.3

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: autorelease: pending

#7 - ci: automatically uploading plasnet results to gh-pages

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

#6 - chore(main): release 0.1.2

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#5 - test: adding integration tests

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

#4 - chore(main): release 0.1.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#3 - ci: adding release-pypi workflow for tagged commits

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

#2 - chore(main): release 0.1.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#1 - Were you tempted to call it planet?

Issue - State: closed - Opened by iqbal-lab over 1 year ago - 1 comment

GitHub / leoisl/plasnet issues and pull requests