Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / baderlab/autoannotateapp issues and pull requests

#207 - Unable to build clustering annotation from the command line

Issue - State: open - Opened by ycaspi257 2 months ago - 13 comments

#205 - Color EM nodes according to cluster

Issue - State: open - Opened by mikekucera 8 months ago
Labels: enhancement

#204 - Hightlight significant node on a subnetwork: it works well!

Issue - State: closed - Opened by veroniquevoisin 8 months ago - 1 comment

#203 - gene-set with larger font per cluster: weird resolution on the pdf

Issue - State: closed - Opened by veroniquevoisin 9 months ago - 5 comments

#202 - blank AA Display

Issue - State: closed - Opened by veroniquevoisin 9 months ago - 21 comments

#200 - Label font size when creating a subnetwork

Issue - State: closed - Opened by veroniquevoisin 10 months ago - 2 comments

#199 - Display Options panel needs a scrollbar

Issue - State: closed - Opened by mikekucera 10 months ago

#198 - still get the double annotation when I try to move an annotation

Issue - State: open - Opened by veroniquevoisin 10 months ago - 2 comments

#197 - annotation sets created in 1.3.5 are incomplete once updating to 1.4.0

Issue - State: closed - Opened by Andre-C-M about 1 year ago - 3 comments

#195 - Upgrade Java and Guice

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

#194 - Change display options defaults

Issue - State: closed - Opened by mikekucera over 1 year ago

#193 - Allow the user to choose the granularity of the clusters

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

#191 - remove dependency on WordCloud

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

#190 - Bump guava from 31.1-jre to 32.0.0-jre in /AutoAnnotate

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

#189 - Better Labels for clusters

Issue - State: open - Opened by mikekucera over 1 year ago - 1 comment

#188 - "Scale" slider in one of the panels

Issue - State: closed - Opened by mikekucera over 1 year ago

#187 - Ellipses duplicated when a cluster is moved

Issue - State: open - Opened by veroniquevoisin over 1 year ago - 2 comments

#186 - Add section to docs explaining cluster selection

Issue - State: closed - Opened by mikekucera almost 2 years ago - 1 comment
Labels: docs

#185 - Is there a toggle to turn on and off connection between annotations and clusters?

Issue - State: closed - Opened by risserlin almost 2 years ago - 1 comment
Labels: question

#184 - Update creation dialog after dependency app is installed

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

#183 - question? aggregated summary

Issue - State: closed - Opened by veroniquevoisin almost 2 years ago - 6 comments

#182 - Add support for MCODE

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

#180 - Add a 'reset' button to the display options panel

Issue - State: closed - Opened by mikekucera about 2 years ago

#179 - enhancement style: add a slide bar to reduce ellipse size?

Issue - State: closed - Opened by veroniquevoisin about 2 years ago - 1 comment
Labels: enhancement

#178 - Repeated deleting nodes causes AutoAnnotate to break

Issue - State: closed - Opened by mikekucera about 2 years ago

#176 - enhancement style: add different colors to ellipses

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

#175 - Bump gson from 2.6.2 to 2.8.9 in /AutoAnnotate

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

#174 - clusterMaker algorithm "Cluster Fuzzifier" not working.

Issue - State: closed - Opened by mikekucera almost 3 years ago - 1 comment
Labels: bug

#173 - No easy way to see the different dataset colours once created a summary network

Issue - State: closed - Opened by risserlin about 3 years ago - 1 comment
Labels: enhancement

#172 - Summary network from Dataset coloured network

Issue - State: closed - Opened by risserlin about 3 years ago - 3 comments
Labels: bug, enhancement

#171 - summary network : not able to set node size attribute

Issue - State: closed - Opened by veroniquevoisin about 3 years ago - 6 comments

#170 - When I create summary network, how are the resulting metanodes colored?

Issue - State: closed - Opened by sylee20 over 3 years ago - 1 comment

#169 - On session reload I loose all style over-rides for collapsed network

Issue - State: closed - Opened by risserlin over 3 years ago - 1 comment
Labels: bug

#167 - need to set Edge weight column to

Issue - State: closed - Opened by veroniquevoisin over 3 years ago

#165 - Collapse nework with post analysis edges - meta edges have no info

Issue - State: closed - Opened by risserlin over 3 years ago - 2 comments
Labels: enhancement

#164 - wordcloud minimum word occurrence

Issue - State: closed - Opened by pillepalle123 over 3 years ago - 12 comments
Labels: enhancement, wordcloud dependency

#163 - manually change label --> recalculate labels and loose all my changed labels

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

#162 - Layout Clusters

Issue - State: closed - Opened by pillepalle123 over 3 years ago - 7 comments

#161 - Update App to Java 11

Issue - State: closed - Opened by mikekucera over 3 years ago
Labels: bug

#160 - Columns created after opening dialog are not included in list.

Issue - State: closed - Opened by veroniquevoisin over 3 years ago - 4 comments
Labels: bug

#159 - AA collapse all clusters a bunch of nodes together in one spot

Issue - State: open - Opened by risserlin almost 4 years ago
Labels: bug

#158 - hidden edges: cannot use autoannotate, created a subnetwork as a workaround

Issue - State: closed - Opened by veroniquevoisin about 4 years ago - 6 comments

#156 - Bump junit from 4.11 to 4.13.1 in /AutoAnnotate

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

#155 - Add ability to provide user assigned clusters to label-clusterBoosted

Issue - State: closed - Opened by s2hui about 4 years ago - 1 comment

#154 - autoannotate layout command

Issue - State: closed - Opened by risserlin over 4 years ago - 2 comments
Labels: enhancement

#153 - Not showing new columns in dropdown to select user-defined clusters

Issue - State: closed - Opened by risserlin over 4 years ago - 1 comment
Labels: bug

#152 - My entire network annotated was deleted

Issue - State: closed - Opened by apostonaut over 4 years ago - 1 comment

#151 - "Ghost" annotate cluster bubbles

Issue - State: closed - Opened by shraddhapai almost 5 years ago - 4 comments
Labels: bug

#149 - autoannotate option returnJsonOnly=true returns nothing

Issue - State: closed - Opened by risserlin almost 5 years ago - 1 comment
Labels: bug

#148 - Collapse all restructures network layout

Issue - State: closed - Opened by gaelanm almost 5 years ago - 2 comments

#147 - mcl cluster: granularity parameter (inflatation value)

Issue - State: closed - Opened by veroniquevoisin about 5 years ago - 1 comment
Labels: enhancement

#146 - Fetch nodes belonging to AutoAnnotate clusters via CyREST API

Issue - State: closed - Opened by rosscm about 5 years ago - 4 comments

#145 - "select cluster" action in context menu

Issue - State: closed - Opened by mikekucera about 5 years ago
Labels: enhancement

#144 - AutoAnnotate problems with generating annotated cluster

Issue - State: closed - Opened by mikekucera over 5 years ago

#143 - enhancement: be able to autoannotate on selected nodes only

Issue - State: closed - Opened by veroniquevoisin over 5 years ago - 2 comments

#142 - Annotation Names

Issue - State: closed - Opened by AshleyHeinson over 5 years ago - 3 comments

#141 - Scale font by cluster: reduce the difference between min and max size

Issue - State: closed - Opened by veroniquevoisin over 5 years ago - 1 comment

#140 - Layout clusters to prevent overlap via command-line

Issue - State: closed - Opened by Niveda-S over 5 years ago - 4 comments
Labels: enhancement

#139 - Not able to use "User-defined clusters"

Issue - State: closed - Opened by veroniquevoisin almost 6 years ago - 1 comment

#138 - Summary Network: edge table is empty

Issue - State: closed - Opened by mikekucera almost 6 years ago
Labels: bug

#137 - Selected annotation not removed

Issue - State: closed - Opened by mikekucera about 6 years ago
Labels: bug

#135 - exclusion of words

Issue - State: closed - Opened by veroniquevoisin about 6 years ago - 3 comments
Labels: enhancement

#134 - Is there a margin around the annotations?

Issue - State: closed - Opened by risserlin about 6 years ago - 1 comment
Labels: enhancement, question

#132 - Export Gene Lists

Issue - State: closed - Opened by mikekucera over 6 years ago
Labels: enhancement

#130 - Layout clusters to prevent overlap.

Issue - State: closed - Opened by mikekucera over 6 years ago - 1 comment
Labels: enhancement

#122 - Played with the EM Q-Value on an autoannotated EM: Cytoscape is frozen

Issue - State: closed - Opened by veroniquevoisin almost 7 years ago - 1 comment

#121 - stored session: cannot play with the "Autoannotate display"

Issue - State: closed - Opened by veroniquevoisin almost 7 years ago - 1 comment

#119 - update documentation for 1.3

Issue - State: closed - Opened by mikekucera almost 7 years ago - 1 comment
Labels: enhancement

#118 - make AutoAnnotate open Wordcloud automatically

Issue - State: closed - Opened by veroniquevoisin almost 7 years ago - 1 comment

#112 - meta-edges created by AutoAnnotate question

Issue - State: closed - Opened by ctekellogg about 7 years ago - 4 comments
Labels: duplicate, enhancement

#111 - accidentally expanded collapsed cluster with double click, can't re-collapse it

Issue - State: closed - Opened by risserlin about 7 years ago - 2 comments
Labels: bug

#110 - add ability to communicate with autoannotate with cyrest

Issue - State: closed - Opened by risserlin about 7 years ago - 4 comments
Labels: enhancement

#108 - Hidden labels and annotations still present in exported PDF

Issue - State: closed - Opened by risserlin over 7 years ago - 3 comments
Labels: bug

#100 - quick start top 10 clusters different from full version.

Issue - State: closed - Opened by risserlin over 7 years ago
Labels: bug

#99 - Max number of clusters on quick start has no effect

Issue - State: closed - Opened by mikekucera over 7 years ago
Labels: bug

#98 - change default to 3 words for annotation

Issue - State: closed - Opened by risserlin over 7 years ago
Labels: enhancement

#97 - Annotating large network crashes cytoscape

Issue - State: closed - Opened by mikekucera over 7 years ago - 2 comments
Labels: bug, cytoscape-bug

#96 - It would be nice to allow any column to be the label column

Issue - State: closed - Opened by mcsimenc over 7 years ago - 2 comments

#95 - Collapsing clusters does not remove annotations

Issue - State: closed - Opened by mikekucera over 7 years ago
Labels: bug

#94 - enable autoannotate collapse/expand all command

Issue - State: closed - Opened by risserlin over 7 years ago - 1 comment
Labels: enhancement

#93 - annotations are sporadically and randomly placed in far corners of pane

Issue - State: closed - Opened by risserlin over 7 years ago - 3 comments
Labels: bug

#92 - Add redraw annotations to aa command options

Issue - State: closed - Opened by risserlin over 7 years ago
Labels: enhancement

#91 - Autoannotate command with network specified but network is not current network returns error

Issue - State: closed - Opened by risserlin over 7 years ago - 3 comments
Labels: bug

#90 - autoannotation of an EM with post-analysis

Issue - State: closed - Opened by veroniquevoisin over 7 years ago - 2 comments
Labels: duplicate, enhancement

#89 - different defaults when running aa from the command line

Issue - State: closed - Opened by risserlin over 7 years ago - 8 comments
Labels: bug

#88 - Exclude post analysis edges and nodes from annotation calculation

Issue - State: closed - Opened by risserlin over 7 years ago - 9 comments
Labels: enhancement

#87 - can't redraw or delete annotations on a reopened previously saved session

Issue - State: closed - Opened by veroniquevoisin over 7 years ago - 1 comment
Labels: bug

#86 - label order sometimes different for cyrest command and summary network

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

#85 - Show Display Options panel when creating an annotation set

Issue - State: closed - Opened by mikekucera over 7 years ago
Labels: bug