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Inclusion of all changes made during the 2024 internship #11

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Inclusion of all changes made during the 2024 internship #11

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tsertijn
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@tsertijn tsertijn commented Jul 5, 2024 •
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crfmc and others added 30 commits March 5, 2024 14:51
@crfmc
feat: make CNV file optional (hms-dbmi#132)
86a6e51
@sehilyi
fix: cnv track
4c9f8bc
@dominikglodzikhms
Update README.md
4a550fd
@dominikglodzikhms
Update README.md
f98d0a9
@dominikglodzikhms
Update README.md
822f4c6
@sehilyi
Update index.md
ae0fc4f
@sehilyi
fix: update PTEN position based on hg38 (hms-dbmi#140)
bf82344
@sehilyi
feat: make pe_support optional in sv bedpe data (hms-dbmi#137)
3104b02
@dominikglodzikhms
Update driver.custom.json
83c293a
@dominikglodzikhms
Update genome-view.md
b00adca
@sehilyi
feat: upgrade gosling.js to 0.17.0 (hms-dbmi#143)
4d0191d
@crfmc
feat: minimal_mode for iframe embedding (hms-dbmi#138)
d1c1969
@tsertijn
Create baf
3c6278e
@tsertijn
Rename baf to baf.ts
9b141e8
@tsertijn
Update baf.ts
8657d2e 
start coding
@tsertijn
Delete src/track directory
a9259b0
@tsertijn
Add files via upload
bed22cf 
edited files were annoying with git
@tsertijn
Delete src/App.tsx
2663345 
problems git push
@tsertijn
Add files via upload
eeb8f80
@tsertijn
Add files via upload
915bf0d
@tsertijn
Add files via upload
7ee40ba
@tsertijn
Delete src/mid-spec.ts
6bdc6ca
@tsertijn
Add files via upload
5178320
@tsertijn
Update samples.ts
14e5d26 
added rout to include BAF
test
fca41b2
@tsertijn
Update main.tsx to include the dev/codec path instead of app
d136da7
@tsertijn
Update vite.config.ts to allow for the dev/codec to work
b5876dc
hope is a nice thing
df1c8f1
@crfmc @sehilyi
feat: updates to the minimal mode version (hms-dbmi#146)
4025551 
Co-authored-by: sehilyi <[email protected]>
@sehilyi
Update build-and-deploy.yml
8ae8b20
nicolasdebusschere and others added 15 commits August 29, 2024 09:45
@nicolasdebusschere
Add changes to cnv track so that the segmented mean also shows up in …
72590ad 
…different colors and changed the samplesize for the haplo track
@Maximvan
New tracks and summary view
1aa562b
@Maximvan
Merge branch 'main' of https://github.com/tsertijn/chromoscope
33b2c95
@nicolasdebusschere
Merge remote-tracking branch 'upstream/main'
c5eabee
@Maximvan
Update question mark placement to be responsive with tracks shown
f4139d1
@nicolasdebusschere
Add inline to cnv track
9175c58
@Maximvan
Fixing Layout of main specs and region search.
630dfce
@nicolasdebusschere
Merge branch 'main' of https://github.com/tsertijn/chromoscope
9944452
@nicolasdebusschere
add explanation and popover images for CNV, haplo and BAF
2817fec
@nicolasdebusschere
Merge branch 'main' of https://github.com/tsertijn/chromoscope
3c35de0
@nicolasdebusschere
Customized genome and variant view
b1f4842
@Maximvan
Layout changes
e66efe0
@Maximvan
Merge branch 'main' of https://github.com/tsertijn/chromoscope
647a506
@tsertijn
added a track to run baf as from a higlass server, these changes also…
dda9b31 
… contain a part in scrits that contains a bash script for creating and uploading the file to a local higlass from a tsv originating from hopla
@tsertijn
Update create_all_files_for_multivec_formatting.py
62fae2b 
added notes to make the script clearer
@tsertijn tsertijn changed the title inclussion of working BAF inclussion of all changes made during the 2024 internship Sep 5, 2024
@tsertijn tsertijn changed the title inclussion of all changes made during the 2024 internship Inclusion of all changes made during the 2024 internship Sep 5, 2024
@nicolasdebusschere
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Overview of the workflow from hopla to chromoscope

Workflow_Internship

@matthdsm matthdsm changed the base branch from master to dev October 1, 2024 08:27
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6 participants
@tsertijn @nicolasdebusschere @crfmc @sehilyi @dominikglodzikhms @Maximvan