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BaderLab
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AutoAnnotateApp
The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.
GNU Lesser General Public License v2.1
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Unable to build clustering annotation from the command line
#207
ycaspi257
opened
1 week ago
13
autoannotate-1.5.1-SNAPSHOT: Cytoscape freezes when I play with AA parameters (Annotation Display)
#206
veroniquevoisin
opened
4 months ago
0
Color EM nodes according to cluster
#205
mikekucera
opened
5 months ago
0
Hightlight significant node on a subnetwork: it works well!
#204
veroniquevoisin
closed
5 months ago
1
blank AA Display
#202
veroniquevoisin
closed
5 months ago
21
enhancement: add option to label modules using the most significant genesets
#201
veroniquevoisin
closed
6 months ago
1
gene-set with larger font per cluster: weird resolution on the pdf
#203
veroniquevoisin
closed
6 months ago
5
Display Options panel needs a scrollbar
#199
mikekucera
closed
7 months ago
0
Label font size when creating a subnetwork
#200
veroniquevoisin
closed
7 months ago
2
still get the double annotation when I try to move an annotation
#198
veroniquevoisin
opened
7 months ago
2
annotation sets created in 1.3.5 are incomplete once updating to 1.4.0
#197
Andre-C-M
closed
1 year ago
3
label of the most significant node in a cluster should be significantly larger
#196
mikekucera
closed
12 months ago
0
Upgrade Java and Guice
#195
mikekucera
opened
1 year ago
0
Change display options defaults
#194
mikekucera
closed
1 year ago
0
Allow the user to choose the granularity of the clusters
#193
mikekucera
closed
11 months ago
2
Add option to use the node with the highest significance as the label for the cluster
#192
mikekucera
closed
1 year ago
0
remove dependency on WordCloud
#191
mikekucera
closed
1 year ago
1
Bump guava from 31.1-jre to 32.0.0-jre in /AutoAnnotate
#190
dependabot[bot]
opened
1 year ago
0
Better Labels for clusters
#189
mikekucera
opened
1 year ago
1
"Scale" slider in one of the panels
#188
mikekucera
closed
1 year ago
0
Ellipses duplicated when a cluster is moved
#187
veroniquevoisin
opened
1 year ago
2
Add section to docs explaining cluster selection
#186
mikekucera
closed
1 year ago
1
Is there a toggle to turn on and off connection between annotations and clusters?
#185
risserlin
closed
1 year ago
1
Update creation dialog after dependency app is installed
#184
mikekucera
closed
1 year ago
0
question? aggregated summary
#183
veroniquevoisin
closed
1 year ago
6
Add support for MCODE
#182
mikekucera
closed
12 months ago
0
"User defined clusters" combo box does not update when new columns are created
#181
mikekucera
closed
1 year ago
0
Add a 'reset' button to the display options panel
#180
mikekucera
closed
1 year ago
0
enhancement style: add a slide bar to reduce ellipse size?
#179
veroniquevoisin
closed
1 year ago
1
Repeated deleting nodes causes AutoAnnotate to break
#178
mikekucera
closed
1 year ago
0
difficulty with autoannotate after we reduced the number of enrichmentmap edges using the EM slidebar
#177
veroniquevoisin
closed
1 year ago
8
enhancement style: add different colors to ellipses
#176
veroniquevoisin
closed
1 year ago
2
Bump gson from 2.6.2 to 2.8.9 in /AutoAnnotate
#175
dependabot[bot]
opened
2 years ago
0
clusterMaker algorithm "Cluster Fuzzifier" not working.
#174
mikekucera
closed
1 year ago
1
No easy way to see the different dataset colours once created a summary network
#173
risserlin
closed
1 year ago
1
Summary network from Dataset coloured network
#172
risserlin
closed
2 years ago
3
summary network : not able to set node size attribute
#171
veroniquevoisin
closed
2 years ago
6
When I create summary network, how are the resulting metanodes colored?
#170
sylee20
closed
2 years ago
1
On session reload I loose all style over-rides for collapsed network
#169
risserlin
closed
3 years ago
1
need to set "Edge weight column" to "None" otherwise, no annotations is created, I don't know the reason
#168
veroniquevoisin
closed
2 years ago
11
need to set Edge weight column to
#167
veroniquevoisin
closed
3 years ago
0
post analysis edges + annotations very buggy - loosing nodes from the main network, randomly creating duplicates of nodes
#166
risserlin
opened
3 years ago
10
Collapse nework with post analysis edges - meta edges have no info
#165
risserlin
closed
1 year ago
2
wordcloud minimum word occurrence
#164
pillepalle123
closed
3 years ago
12
manually change label --> recalculate labels and loose all my changed labels
#163
risserlin
closed
3 years ago
1
Layout Clusters
#162
pillepalle123
closed
2 years ago
7
Update App to Java 11
#161
mikekucera
closed
3 years ago
0
Columns created after opening dialog are not included in list.
#160
veroniquevoisin
closed
3 years ago
4
AA collapse all clusters a bunch of nodes together in one spot
#159
risserlin
opened
3 years ago
0
hidden edges: cannot use autoannotate, created a subnetwork as a workaround
#158
veroniquevoisin
closed
1 year ago
6
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