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Merge DIGGER 2.0 into main #53

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Merge DIGGER 2.0 into main #53

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Eeeeelias
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Many changes, including:

  • Option to explore mouse data
  • Ability to use predicted Domain-Domain Interactions (DDIs)
  • Do NEASE analysis in the web
  • Ability to search for multiple terms simultaneously
  • New and improved UI/UX
  • Pipeline for predicting DDIs from PPIs
  • Structure to easily add more model organisms to explore
  • Time optimizations to data processing
  • Many bug fixes

ChumlerNg and others added 30 commits March 9, 2023 04:38
@ChumlerNg
Extend with mouse data
5e3e721 
Changes to code to enable the extension with mouse data
@ChumlerNg
Update network_analysis.py
7599a7d 
small fix
@ChumlerNg
Update requirements.txt
e8c71ba
@ChumlerNg
Updating Pfam links to interpro
d03f331
file restructuring start
d3732d5
more dynamic read in of organism files
ad19eed
restructuring of database to allow for more dynamic access
7970a77
Added js files with common functions
ba1b064
take out the final human/mouse specific implementations
56449ba
@Eeeeelias
fixed selected element
4ef9aed
@Eeeeelias
use regex instead of positional checking for IDs
cfdd33f
@Eeeeelias
formatting & spelling
1768bba
@Eeeeelias
improved regexes to be more specific
9048b65 
removed last bits of hardcoded organism code
@Eeeeelias
more formatting
f5b631c
@Eeeeelias
temporarily added extended data as default
eb60968
@Eeeeelias
added base annotations to DomainG and DDI
4e11e84
@Eeeeelias
formatting + adapting code to predictions
b388242
@Eeeeelias
predicted edges are now yellow
c58630d
@Eeeeelias
predicted/original edges button now works rudimentary in transcript d…
e42fd7e 
…omainview
@Eeeeelias
[borked commit] converting arrays to dictionaries/objects
c08fe82
@Eeeeelias
change to dictionaries in DomainView
5f1acfd
@Eeeeelias
refactored to accustom high, medium and low confidence interactions
094a88f
@Eeeeelias
formatting + first changes to ProteinView and InteractionView to supp…
d83d8a1 
…ort predicted interactions
@Eeeeelias
added predicted buttons to all transcript views with abstracted JS
1a80290
@Eeeeelias
split up interactions in InteractionView select box
80cc244
@Eeeeelias
graph no longer updates if the edges don't change
8bd8c4b
@Eeeeelias
transcript view now works properly with predicted data
76789ed
@Eeeeelias
updated all parts of the website to include predicted interactions
6448fa0
@Eeeeelias
adjusted images
8a6142f
@Eeeeelias
adjusted image legends
e4539d8
Eeeeelias and others added 27 commits August 5, 2024 10:58
@Eeeeelias
add quick analyse functionality
149aba6
@Eeeeelias
update tooltips on page change
0aedfce
@Eeeeelias
revert db production host
ced868d
@Eeeeelias
remove unused tooltip classes
5ff310e
@Eeeeelias
Merge pull request #36 from Eeeeelias/master
ad4ef8e 
Added a quick action to Pathway IDs for easier usage
@Eeeeelias
set min delta of whippet input to 0.3 by default
e978423
@Eeeeelias
formatting
77382ec
@Eeeeelias
Merge pull request #37 from Eeeeelias/master
92bef65 
Change default min delta value for Whippet input
@Eeeeelias
make tables more compatible with the web
d2028db
@Eeeeelias
remove todo
5b29a5e
@Eeeeelias
center tables in overview
f716d58
@Eeeeelias
adjust table size to fit more resolutions
aee3297
@Eeeeelias
Merge pull request #40 from Eeeeelias/master
ac28c35 
Adjusting the data tables
@Eeeeelias
remove pie chart shadow
076b690
@Eeeeelias
more detailed error message when wrong organism
e61eff6
@Eeeeelias
more detailed error message when wrong organism
58cac0f
@Eeeeelias
changed 3d pie chart to be prettier
c59f5f3
@Eeeeelias
Merge pull request #42 from Eeeeelias/master
7867e7f 
Update pie chart and improve error messages
@Eeeeelias
add example data button
8e9ca21
@Eeeeelias
make the button work
6ee0b87
@Eeeeelias
better info text
274a0d9
@Eeeeelias
Improve UX
04c4271
@Eeeeelias
Merge pull request #44 from Eeeeelias/master
b148776 
Add example data for publication
@Eeeeelias
Add more helpful and detailed error messages
bd30bd5
@Eeeeelias
Add more helpful and detailed error messages
9323759
@Eeeeelias
Merge pull request #45 from Eeeeelias/master
9472b2a 
Added more detailed error messages
@Eeeeelias
Merge branch 'master' into DIGGER-v1.7
918bad9
@Eeeeelias Eeeeelias closed this Sep 6, 2024
@Eeeeelias
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Should've gone to daisybio/DIGGER. Ooopsie!

@louadi louadi reopened this Sep 6, 2024
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3 participants
@Eeeeelias @louadi @ChumlerNg