Code

Trinucleotide#2

Code

Merged

andreagulino merged 165 commits intomasterDEIB-GECO/MutViz:masterfrom trinucleotideDEIB-GECO/MutViz:trinucleotideCopy head branch name to clipboardOct 13, 2020

+20,381-1,100

Commits

Commits on Apr 2, 2020

• setup new visualization

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Commits on Apr 27, 2020

• add new views

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• add spark

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• update api

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• fix url

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• use api data

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• set java memory

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• Update intersection.py

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• use spark sql query

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• add binning

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• fix data loss on tumor change

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• Update intersection.py

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Commits on Apr 28, 2020

• Update models.py

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• Update api.py

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• Update intersection.py

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• Update api.py

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• Update api.js

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• Update intersection.py

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Commits on May 4, 2020

• Change db to geco

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• Update api.js

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• Update api.py

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• fix donor api

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Commits on May 5, 2020

• Connect uc5

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• Add cache for uc5

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Commits on May 6, 2020

• implement uc6 backed

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• fix cache for signatures

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Commits on May 7, 2020

• average on donors for signatures

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• Update api.py

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• remove debug prints

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Commits on May 8, 2020

• Use prevalence instead of exposure

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• remove debug logging

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• add box-plot for signatures

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• add download data option

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• Update api.py

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Commits on May 11, 2020

• improve frontend with plot button

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• add min 1000 mutations merge ifl 5 tumors

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• fix missing api update

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• remove logging

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• fix sum series to dataframe

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• Update api.js

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• Update intersection.py

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• Add threshold as an option

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• fix cache problem

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• avoid cached pages

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• Update api.py

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• optimize retrieve time

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• Update api.py

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Commits on May 12, 2020

• fix laoding error

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• set threshold to 0 when disabled

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Commits on May 13, 2020

• rename box plot view to donor distribution

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• round box plot min and max values

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• warn when there are not enough patients

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• describe the threshold

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• implement donor distribution on trinucleotides

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• fix cache bug

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• stop loading when errors occur

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• Update api.py

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• fix bug in intersect due to wrong spark partitioning

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Commits on May 14, 2020

• add spark debug option

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• fix env name

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• implement intersection with groupby

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• log begin of processing

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• add time elapsed when logging

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• Update intersection.py

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• Update intersection.py

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• Update intersection.py

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• fix threshold filtering

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• back to mappartitions without chromosome constraint

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• deepcopy regions and debug partitions

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• add fs db option

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• set schema when importing csv

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• Update intersection.py

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Commits on May 18, 2020

• Add new refitting

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• bug fix

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• re-enable cache for signatures

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• remove casting to int

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• Update signatures_refitting.py

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• convert chromosome from int to string

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• Update signatures_refitting.py

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• Update signatures_refitting.py

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• Update signatures_refitting.py

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Commits on May 19, 2020

• Allow custom region file

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• Update signatures_refitting.py

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• Update signatures_refitting.py

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• Update signatures_refitting.py

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• add memory cache to signatures

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• add cache for other calls

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• return at cache hit

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Commits on May 20, 2020

• Create delete_cache.sql

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• Update repository.py

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• fix slider

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• fix slider

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Commits on May 21, 2020

• Update donors.py

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• lowercase regions name to generate the id

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• remove special characters from regions id

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• Update repository.py

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• show name instead of identifier in regions heatmap

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• Update uc2-controller.js

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• fix mutation type issuo in uc3

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Commits on May 26, 2020

• Add mutation filter popup

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Commits on Jun 1, 2020

• Update __init__.py

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• exclude chromosome X and Y from refitting

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Commits on Jun 8, 2020

• Download PNG and filter by clinical condition

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• fix filter

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• disable debug mode

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• Update signature.py

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• Update signature.py

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• Update signature.py

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• fix caching

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• Test unique cache for intersection

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• Update trinucleotide.py

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• Update trinucleotide.py

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• Update trinucleotide.py

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• Update trinucleotide.py

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• Update trinucleotide.py

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• Update trinucleotide.py

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• new donors implementation

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• Update donors.py

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• Update donors.py

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• new signatures implementation

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• Update signature.py

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• clean models

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Commits on Jun 9, 2020

• debug signature refitting time

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• Update signatures_refitting.py

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• try ddask

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• Update signatures_refitting.py

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• Update signatures_refitting.py

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• fix cache

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• Implemente new test

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• switch debug false

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• re-map clinical data tumor type id

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• update version

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• Update style.css

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Commits on Jun 17, 2020

• Update main-controller.js

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• Update main-controller.js

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Commits on Jun 20, 2020

• Update descriptions in the home page and in each view

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• Update uc6.html

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Commits on Jun 23, 2020

• fix duplicate files added to workspace

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• remove old download method

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• set num regions limit for old views

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Commits on Jun 24, 2020

• Add repo description

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• fix descriptions + normalization and color range

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Commits on Jun 25, 2020

• fix testing

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• update version

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Commits on Jun 26, 2020

• Fix text

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• Fix image download

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Commits on Jun 27, 2020

• Update version

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• Update uc5.js

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Commits on Jul 1, 2020

• Add intro image

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• Create intro-full.png

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• update images

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• Update intro.png

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• Update uc6.js

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