Ecosyste.ms: Issues

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GitHub / molgenis/capice-resources issues and pull requests

#90 - 5.1.2 v4 validation

Pull Request - State: closed - Opened by bartcharbon 2 months ago - 1 comment

#89 - Update dependencies

Pull Request - State: closed - Opened by bartcharbon 2 months ago - 1 comment

#88 - New model based on new VKGL and ClinVar resources + fixes in train utility script

Pull Request - State: closed - Opened by bartcharbon 4 months ago - 1 comment

#87 - Bump scikit-learn from 1.2.1 to 1.5.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#86 - Chore/512plots

Pull Request - State: closed - Opened by bartcharbon 11 months ago - 1 comment

#85 - Add 5.1.2 validation plots

Pull Request - State: closed - Opened by bartcharbon 11 months ago - 1 comment

#84 - Improvements and fixes for automation of model training

Pull Request - State: closed - Opened by bartcharbon 11 months ago - 1 comment

#83 - Feat/alpha missense

Pull Request - State: closed - Opened by bartcharbon 11 months ago - 1 comment

#82 - GRCh38 support only + remove GnomadHN

Pull Request - State: closed - Opened by bartcharbon about 1 year ago - 1 comment

#81 - README fixes

Pull Request - State: closed - Opened by bartcharbon over 1 year ago - 1 comment

#80 - chore: CAPICE 5.2.0 release

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#79 - fix: Flipped model 1 and 2 in violinplots

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#78 - [compare-model-performance] Model 1 and model 2 violinplot can be flipped

Issue - State: closed - Opened by SietsmaRJ over 1 year ago
Labels: bug

#77 - Feat/singular model plots

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#76 - Feat/unbiased comparison validation file

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#75 - Feat/more vkgl clinvar data

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 4 comments

#74 - chore: GnomAD HN Model Validation plots

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#73 - fix: Pathogenic label violinplot incorrect

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#72 - [compare-model-performance] Violinplot x axis labels seem flipped

Issue - State: closed - Opened by SietsmaRJ over 1 year ago
Labels: bug

#71 - Fix/python3.11 support

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#70 - fix: Support for patch1 VIP custom gnomad file

Pull Request - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment

#69 - Matplotlib fails to install

Issue - State: closed - Opened by SietsmaRJ over 1 year ago - 1 comment
Labels: bug

#68 - New ClinVar release (20230430) is not supported (error thrown)

Issue - State: closed - Opened by svandenhoek almost 2 years ago
Labels: bug

#67 - fix: Unsupported alt contigs

Pull Request - State: closed - Opened by SietsmaRJ almost 2 years ago - 1 comment

#66 - feat: Additional VCF metadata

Pull Request - State: closed - Opened by SietsmaRJ almost 2 years ago - 1 comment

#64 - feat: Add bind flag pipe to apptainer

Pull Request - State: closed - Opened by SietsmaRJ almost 2 years ago - 2 comments

#63 - feat: Picard 3.0.0 support

Pull Request - State: closed - Opened by SietsmaRJ almost 2 years ago - 2 comments

#62 - Fix for plot paths giving very long string (that doesn't always fit)

Pull Request - State: closed - Opened by svandenhoek almost 2 years ago - 2 comments

#61 - Update setup.py

Pull Request - State: closed - Opened by svandenhoek almost 2 years ago - 1 comment

#60 - chore: 5.0.0 release

Pull Request - State: closed - Opened by SietsmaRJ almost 2 years ago - 2 comments

#59 - Optimized slurm time to match the used cluster queue's.

Pull Request - State: closed - Opened by svandenhoek almost 2 years ago - 1 comment

#58 - Raise error instead of warning "unknown review status ClinVar"

Issue - State: open - Opened by SietsmaRJ almost 2 years ago
Labels: enhancement

#57 - fix: Violinplot split error

Pull Request - State: closed - Opened by SietsmaRJ almost 2 years ago - 1 comment

#56 - compare-model-performance crashes on violinplot when empty dataframe is supplied

Issue - State: closed - Opened by SietsmaRJ almost 2 years ago
Labels: bug

#55 - Train-data-creator doesn't use SYMBOL ID's

Issue - State: open - Opened by SietsmaRJ almost 2 years ago
Labels: bug

#54 - Train-data-creator doesn't take multiple SYMBOL (ID's) into account

Issue - State: open - Opened by SietsmaRJ almost 2 years ago
Labels: bug

#53 - docs: Fixed README typo.

Pull Request - State: closed - Opened by svandenhoek almost 2 years ago - 1 comment

#52 - docs:add acknowledgements

Pull Request - State: closed - Opened by dennishendriksen almost 2 years ago - 1 comment

#51 - fix: ClinVar SYMBOL ID in export VCF ID column

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 1 comment

#50 - chore: Update and equalize dependencies

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 1 comment

#49 - Minor adjustment to README.

Pull Request - State: closed - Opened by svandenhoek about 2 years ago

#48 - Refactor/improved code structure

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 1 comment

#47 - Refactor/improved code structure

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 1 comment

#46 - Added github templates.

Pull Request - State: closed - Opened by svandenhoek about 2 years ago - 2 comments

#45 - Feat/travis

Pull Request - State: closed - Opened by svandenhoek about 2 years ago - 3 comments

#44 - chore: Bump dependency versions

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 1 comment

#43 - feat: Validation 5.0.0-v2

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 1 comment

#42 - Security vulnerabilities

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

#41 - Feat/improved duplicate checking

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago

#40 - Feat/compare models qol

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago

#39 - feat: Validation homozygosity counts

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 2 comments

#38 - Feat/improved validation dataset

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago - 1 comment

#37 - Feat/violinplots

Pull Request - State: closed - Opened by SietsmaRJ about 2 years ago

#36 - fix/readme_update_public_vkgl

Pull Request - State: closed - Opened by svandenhoek about 2 years ago

#35 - Feat/expanded threshold

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#34 - Fix README layout

Pull Request - State: closed - Opened by svandenhoek over 2 years ago

#33 - feat: Public VKGL

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#32 - Feat/af bin validation

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#31 - fix: gitignore

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#30 - Feat/simplified bcftools

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago - 1 comment

#29 - Validation 4.0.0

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#28 - Feat: ar gene filtering

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago - 1 comment

#27 - liftover_variants.sh not removing index file

Issue - State: open - Opened by svandenhoek over 2 years ago
Labels: bug

#26 - feat: Calculate threshold

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago - 1 comment

#24 - fix: Amount of samples in AUC.png

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#23 - AUC.png shows incorrect number of samples

Issue - State: closed - Opened by SietsmaRJ over 2 years ago

#22 - No imputing

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#21 - Hotfix for pip install

Pull Request - State: closed - Opened by svandenhoek over 2 years ago

#20 - Pip won't build on master!

Issue - State: closed - Opened by svandenhoek over 2 years ago - 3 comments
Labels: bug

#19 - Fix/comparison scripts

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago - 1 comment

#18 - Fix for separator conflicting with certain gene symbol

Pull Request - State: closed - Opened by svandenhoek over 2 years ago - 3 comments

#17 - Fix/update train process steps + minor fixes/additions

Pull Request - State: closed - Opened by svandenhoek over 2 years ago - 1 comment

#16 - fix: ClinVar review status

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#15 - When running train_data_creator I get error

Issue - State: open - Opened by marikaris over 2 years ago - 1 comment
Labels: bug

#14 - Comparison scripts not functioning out-of-the-box

Issue - State: closed - Opened by svandenhoek over 2 years ago - 1 comment
Labels: bug

#13 - fix: Pseudo allele frequency

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago - 1 comment

#12 - fix: Conflicting consensi

Pull Request - State: closed - Opened by SietsmaRJ over 2 years ago

#11 - GeneSymbols with `_` causes invalid formatted ID field.

Issue - State: closed - Opened by svandenhoek over 2 years ago - 2 comments
Labels: bug

#10 - train_data_creator: Better handling of duplicates.

Issue - State: open - Opened by svandenhoek over 2 years ago
Labels: enhancement

#8 - Bump numpy from 1.21.4 to 1.22.0

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

#7 - feat: Build 37 build 38 model comparison

Pull Request - State: closed - Opened by SietsmaRJ almost 3 years ago

#6 - Train CAPICE models using SpliceAI masked instead of raw data

Issue - State: closed - Opened by dennishendriksen almost 3 years ago - 1 comment
Labels: enhancement

#5 - fix: Windows testing

Pull Request - State: closed - Opened by SietsmaRJ almost 3 years ago

#4 - Testing for Windows fail

Issue - State: closed - Opened by SietsmaRJ almost 3 years ago

#3 - Feature/model creation

Pull Request - State: closed - Opened by svandenhoek about 3 years ago

#2 - Feature/validation figures

Pull Request - State: closed - Opened by svandenhoek about 3 years ago

#1 - Fix/gitignore

Pull Request - State: closed - Opened by svandenhoek about 3 years ago