v0.3.0

What's Changed

• Improve the MTC user guide section by @ielis in #234
• Updates all the notebooks to use gpsea by @lnrekerle in #235
• Create de Vries scorer, support wrapping phenotype scoring function by @ielis in #232
• Handle inheritance modes by @ielis in #239
• Prevent creating a cohort from individuals who include duplicates by @lnrekerle in #238
• Simplify phenopacket loading functions by @ielis in #242
• Add T test by @ielis in #243
• Remove obsolete analysis code by @ielis in #244
• Allow using Sex and disease diagnosis as a genotype predicate by @ielis in #245

Full Changelog: v0.2.0...v0.3.0

v0.2.0

A lot of progress was made since the last version.

What's Changed

• Prepare logic for fetching transcript regions for visualization by @ielis in #67
• Fixed bugs that came up with a subjects in RPGRIP by @lnrekerle in #68
• Finish extending transcript exon model by @ielis in #70
• Set is_preferred annotation by @ielis in #74
• Moved VariantEffects so it's using the Enum by @lnrekerle in #78
• HGVSVariantCoordinatesFinder by @frehburg in #77
• Created Cohort Viewer that shows excluded patients by @lnrekerle in #85
• Fix change length bug by @ielis in #94
• Streamline predicate/analysis workflow by @ielis in #88
• Created new file testing groups against each other by @lnrekerle in #99
• Add methods for simple genome arithmetics by @ielis in #101
• Used tqdm to create a progress bar by @lnrekerle in #107
• Improve error messages by @lnrekerle in #96
• Update notebooks by @lnrekerle in #121
• Removing redundant phenopacket generation code by @pnrobinson in #116
• Add files for PPP2R1A by @pnrobinson in #80
• Removing redundant phenopacket gen code SUOX by @pnrobinson in #115
• removing redudant code to gen phenopackets and adding phenopackets fr… by @pnrobinson in #117
• Setup notebook for visualizers by @ielis in #114
• Run notebooks in CI by @ielis in #122
• Formalize handling and reporting of input errors by @ielis in #128
• Fix bug in summarizing errors and warnings of the notepad. by @ielis in #129
• Add visualization prose by @ielis in #125
• Improve protein service by @lnrekerle in #130
• Humanize the analysis runner by @ielis in #131
• Contextualize the count with the cohort size in the G/P result summary by @ielis in #132
• Changed all occurrences of hgvsc_id to hgvs_cdna by @lnrekerle in #138
• Isolate G/P code by @ielis in #136
• Add Disease to Patient by @lnrekerle in #143
• CLDN16 by @pnrobinson in #146
• Draw variants transcript and protein by @pnrobinson in #148
• Fixed the count issue with summarize by @lnrekerle in #145
• Kbg by @pnrobinson in #154
• Added testing for disease predicates by @lnrekerle in #151
• Update the GitHub action names by @ielis in #158
• Use SUOX cohort as a real-life test data, add JSON (de)serialization by @ielis in #157
• Buffer vv response by @pnrobinson in #155
• Mtc by @pnrobinson in #160
• protein drawing by @pnrobinson in #162
• KMT2D by @pnrobinson in #166
• Restore the deleted test_data_dir fixture by @ielis in #168
• Added disease viewable, variant and effect counts by @lnrekerle in #167
• Check protein coordinates by @ielis in #170
• Kmt2 d by @pnrobinson in #169
• Notebooks all work. Small changes so tables look good. by @lnrekerle in #173
• Created ProteinRegionPredicate by @lnrekerle in #175
• Adding new MTC filter that allows the user to specific which term(s) … by @pnrobinson in #177
• More mtc heuristic by @pnrobinson in #178
• fixing template to have blocks appear underneath each other by @pnrobinson in #182
• Create Protein table so users can see list of protein features and coordinates by @lnrekerle in #179
• Merge Protein Visualizer into develop by @frehburg in #184
• Implement variant predicates and allele counter by @ielis in #159
• Created a Formatter by @lnrekerle in #185
• Fix bug in validation of terms to test in "specify terms" MTC strategy by @ielis in #195
• Removed the red background by @lnrekerle in #193
• multiple testing documentation by @pnrobinson in #189
• Add support for large imprecise SVs by @ielis in #196
• Add section about statistical tests into the documentation by @pnrobinson in #198
• Implement IsStructuralVariantPredicate for testing if a variant is an SV by @ielis in #199
• Add CountingPhenotypePredicate by @ielis in #197
• Updating MTC heuristic and documentation by @pnrobinson in #200
• Expanded table of genotypes by @lnrekerle in #205
• Fix some bugs by @ielis in #208
• Implement logical inversion of a variant predicate by @ielis in #206
• Exemplify usage of the counting predicate on RERE cohort by @ielis in #202
• Reporting the number of tests in GenotypePhenotypeAnalysisResult by @lnrekerle in #209
• Fixing "Division by 0" error by @lnrekerle in #214
• Fixed large variants in variant_key and added documentation and a test. by @lnrekerle in #204
• Demonstrate testing correlation between genotype groups and phenotype score by @ielis in #219
• Fix bug in change length calculation for CNVs by @ielis in #220
• Improve phenotype and MTC filtering by @ielis in #221
• Remove name from Phenotype. by @ielis in #224
• updating tutorial documentation by @pnrobinson in #226
• Update tutorial by @ielis in #225
• Do not run notebooks in CI by @ielis in #229
• Change the project name to GPSEA by @ielis in #230
• Split analysis package into analysis types by @ielis in #231

New Contributors

• @frehburg made their first contribution in #77

Full Changelog: v0.1.0...v0.2.0

v0.1.0

First Release