warelab/gramene-genetree-vis issues and pull requests

#127 - How to prepare the json file of gene and tree?

Issue - State: open - Opened by WangDJ09 over 1 year ago

#126 - Bump ejs and react-scripts

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#125 - Bump node-forge and react-scripts

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#124 - Bump lodash-es from 4.17.20 to 4.17.21

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#123 - Bump express from 4.17.1 to 4.18.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#122 - Bump decode-uri-component from 0.2.0 to 0.2.2

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#121 - Bump qs and express

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#120 - Bump loader-utils and react-scripts

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#119 - Bump d3-color and d3-scale

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#118 - Bump async from 2.6.3 to 2.6.4

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#117 - Bump urijs from 1.19.5 to 1.19.11

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#116 - Bump urijs from 1.19.5 to 1.19.10

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#115 - Bump urijs from 1.19.5 to 1.19.9

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#114 - Bump url-parse from 1.4.7 to 1.5.10

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#113 - Bump urijs from 1.19.5 to 1.19.8

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#112 - Bump url-parse from 1.4.7 to 1.5.7

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#111 - Bump follow-redirects from 1.5.10 to 1.14.8

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#110 - Bump handlebars from 4.7.6 to 4.7.7

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#109 - Bump is-email from 1.0.0 to 1.0.1

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#108 - Bump axios from 0.21.1 to 0.21.2

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#107 - Ez curation

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

#106 - Bump urijs from 1.19.5 to 1.19.7

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#105 - Bump axios from 0.18.1 to 0.21.1

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#104 - curation ui

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

#103 - Bump lodash from 4.17.4 to 4.17.21

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#102 - Bump lodash from 4.17.4 to 4.17.19

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

#101 - super-tree info

Issue - State: open - Opened by ajo2995 over 5 years ago

#100 - identity calculation may be off

Issue - State: open - Opened by ajo2995 over 5 years ago

#99 - show representative homolog info in neighborhood view

Issue - State: closed - Opened by ajo2995 over 6 years ago - 1 comment

#98 - sort child nodes by max identity

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

#97 - pass ensembl url as prop

Issue - State: closed - Opened by ajo2995 almost 7 years ago

#96 - add duplication node confidence score

Issue - State: closed - Opened by ajo2995 about 7 years ago - 1 comment

#95 - Touch dnd

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

#94 - add transcript count to gene tree leaf node popup

Issue - State: closed - Opened by ajo2995 about 7 years ago

#93 - gene tree leaf node label config doesn't work on touch screens

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

#92 - remove the vertical lines from the neighborhood axes

Issue - State: closed - Opened by ajo2995 about 7 years ago - 1 comment

#91 - add an on hover event to indicate that clicking on a gene or the neighborhood arrow might do something

Issue - State: closed - Opened by ajo2995 about 7 years ago - 1 comment

#90 - Fix width of popup to cover text competely

Issue - State: closed - Opened by ajo2995 about 7 years ago

#89 - remove transparency on popups

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

#88 - close popup when clicking a link therein

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

#87 - Phyloview

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

#86 - Phyloview boats

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

#85 - Configure node labels

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

#84 - refactored to use clicks, not mouseovers

Pull Request - State: closed - Opened by thomasoniii about 7 years ago

#83 - make the btn-toolbar position apply only here

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

#82 - neighborhoods are backwards

Issue - State: closed - Opened by ajo2995 about 7 years ago
Labels: bug

#81 - identity doesn't update when changing gene of interest

Issue - State: closed - Opened by ajo2995 about 7 years ago
Labels: bug

#80 - Create react app

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

#79 - Create react app

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

#78 - add a spinner while loading

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

#77 - popover position off in firefox

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

#76 - non-phyloview things worth using

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

#75 - let the representative be pruned. fixes #66

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

#74 - render neighborhoods

Issue - State: closed - Opened by ajo2995 over 7 years ago - 1 comment

#73 - Get the data

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

#72 - changed MSA selection

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

#71 - calculate neighborhoods for internal nodes

Issue - State: open - Opened by ajo2995 over 7 years ago - 1 comment

#70 - get neighborhood query

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

#69 - wire up display mode dropdown

Issue - State: closed - Opened by ajo2995 over 7 years ago - 1 comment

#68 - Non svg msa

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

#67 - prune tree by feature

Issue - State: open - Opened by ajo2995 almost 8 years ago

#66 - hide representative homolog when not from a genome of interest

Issue - State: closed - Opened by ajo2995 almost 8 years ago

#65 - position gene of interest at the top

Issue - State: closed - Opened by ajo2995 almost 8 years ago

#64 - allow user to swap the order of child nodes in tree layout

Issue - State: open - Opened by ajo2995 almost 8 years ago

#63 - need more screen space for MSA in gramoogle

Issue - State: closed - Opened by ajo2995 almost 8 years ago - 1 comment

#62 - add zoom to domain button to domain popover

Issue - State: open - Opened by ajo2995 almost 8 years ago

#61 - Display clade descriptions for internal nodes

Issue - State: open - Opened by ajo2995 almost 8 years ago
Labels: enhancement

#60 - more tree expand/collapse functionality

Issue - State: closed - Opened by ajo2995 almost 8 years ago

#59 - popover content too large

Issue - State: open - Opened by ajo2995 almost 8 years ago

#58 - Popovers

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

#57 - gene tree for RFL1 not rendering nicely

Issue - State: closed - Opened by ajo2995 about 8 years ago
Labels: bug

#56 - Ambiguous internal nodes are black

Issue - State: open - Opened by mycrobe about 8 years ago
Labels: enhancement

#55 - Internal nodes with only one visible child are ugly

Issue - State: closed - Opened by mycrobe about 8 years ago
Labels: bug

#54 - What is the purple domain

Issue - State: closed - Opened by mycrobe about 8 years ago - 1 comment
Labels: bug

#53 - 3.0.6 - lodash patch

Pull Request - State: closed - Opened by mycrobe about 8 years ago

#52 - merge dev into master

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

#51 - toggle display labels on gene tree

Issue - State: closed - Opened by ajo2995 over 8 years ago

#50 - Genomes of interest

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

#49 - Domain popovers in wrong place in Firefox.

Issue - State: closed - Opened by mycrobe over 8 years ago
Labels: bug

#48 - Color alignments by domain

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

#47 - Mouse over

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

#46 - adjust alignments if filtering to genomes of interest

Issue - State: closed - Opened by ajo2995 over 8 years ago

#45 - only display genomes of interest

Issue - State: closed - Opened by ajo2995 over 8 years ago

#44 - rework highlighting

Issue - State: closed - Opened by ajo2995 over 8 years ago

#43 - color alignment by domain

Issue - State: closed - Opened by ajo2995 over 8 years ago

#42 - show paralogs in subtree

Issue - State: closed - Opened by ajo2995 over 8 years ago

#41 - representative gene not expanded

Issue - State: closed - Opened by ajo2995 over 8 years ago
Labels: bug

#40 - add triangles marking exon boundaries (on leaf nodes)

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

#39 - Domain annotations

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

#38 - multiple sequence alignment

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

#37 - Compile styles separately from javascript.

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

#36 - Remove node lessify

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

#35 - If no orthologs/paralogs, the vis breaks the page.

Issue - State: closed - Opened by mycrobe over 8 years ago
Labels: bug

#34 - 1.1.3

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

#33 - Representative50

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

#32 - Allow nodes that are expanded by the layout algorithm to be hidden.

Issue - State: closed - Opened by mycrobe over 8 years ago
Labels: enhancement

#31 - highlight species of interest

Issue - State: closed - Opened by ajo2995 over 8 years ago

#20 - Rendering bug in Safari: Expanded clades have giant internal nodes.

Issue - State: closed - Opened by mycrobe over 8 years ago - 1 comment
Labels: bug

#7 - Add different expanded/contracted algorithms

Issue - State: closed - Opened by mycrobe over 8 years ago
Labels: enhancement

#6 - Add option to expand and contract multiple nodes

Issue - State: closed - Opened by mycrobe over 8 years ago
Labels: enhancement

GitHub / warelab/gramene-genetree-vis issues and pull requests