monarch-initiative pheval issues

monarch-initiative / pheval

A framework for empirical evaluation of phenotype matching and prioritisation

https://monarch-initiative.github.io/pheval/

Apache License 2.0

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issues

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Update PhEval Pipeline Documentation

#352 souzadevinicius opened 2 hours ago
0
Update PhEval Pipeline Documentation

#351 souzadevinicius opened 2 hours ago
0
Versioning plan of the corpora

#350 yaseminbridges opened 5 days ago
1
Disease prioritization results benchmarking from different disease ontologies

#349 AO33 opened 2 weeks ago
5
346 duckdb for benchmarking

#348 yaseminbridges opened 3 weeks ago
0
Problems using pheval

#347 seoanezonjic opened 1 month ago
6
DuckDB for benchmarking

#346 yaseminbridges opened 1 month ago
0
Ensure string typing when checking for string/list in gene prioritisation analysis

#345 yaseminbridges closed 1 month ago
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Ensure string typing when checking for list/string in gene benchmarking

#344 yaseminbridges closed 1 month ago
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Update documentation with new PhEval runners

#343 yaseminbridges closed 1 month ago
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Add runners to documentation

#342 yaseminbridges closed 1 month ago
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SOP for pheval releases

#341 matentzn opened 2 months ago
0
339 add synthetic corpus

#340 yaseminbridges opened 2 months ago
0
Add synthetic corpus

#339 yaseminbridges opened 2 months ago
0
Add a pipeline test that invokes pheval.template

#338 souzadevinicius opened 2 months ago
0
Add a pipeline test that invokes pheval.template

#337 souzadevinicius opened 2 months ago
0
Ensure type matching in benchmark for variants

#336 yaseminbridges closed 3 months ago
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Ensure matching between position & chromosome in matching for benchmarking

#335 yaseminbridges closed 3 months ago
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333 allow multiple genes/gene identifiers for a single ranked result

#334 yaseminbridges closed 2 months ago
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Allow multiple genes/gene identifiers for a single ranked result

#333 yaseminbridges closed 2 months ago
0
331 iterate over corpus directory and check for corresponding results when benchmarking

#332 yaseminbridges closed 3 months ago
1
Iterate over corpus directory and check for corresponding results when benchmarking

#331 yaseminbridges closed 3 months ago
0
Fix type checking in extracted results

#330 yaseminbridges closed 3 months ago
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Fix type checking in post processing of results

#329 yaseminbridges closed 3 months ago
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Remove phenopackets with no observed phenotypes

#328 yaseminbridges closed 3 months ago
0
Remove phenopackets with all negated phenotypic terms

#327 yaseminbridges closed 3 months ago
0
325 alter ranking of results penalising results found at the same rank

#326 yaseminbridges closed 3 months ago
2
Alter ranking of results, penalising results found at the same rank

#325 yaseminbridges closed 3 months ago
0
Replace sample ID only in VCF header

#324 yaseminbridges closed 3 months ago
0
Only convert sample ID in the VCF in the header lines.

#323 yaseminbridges closed 3 months ago
0
317 add arguments hg19 vcf dir and hg38 vcf dir to spike vcf command

#322 yaseminbridges closed 3 months ago
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Handle IndexError for spiking variants into a VCF

#321 yaseminbridges closed 3 months ago
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Index error in create spiked VCF command

#320 yaseminbridges closed 3 months ago
0
Write out phenopackets if not updating gene identifiers in `prepare-corpus` command

#319 yaseminbridges closed 4 months ago
0
Write out phenopackets in `prepare-corpus` even if not updating gene symbol

#318 yaseminbridges closed 4 months ago
0
Add arguments `--hg19-vcf-dir` and `--hg38-vcf-dir` to spike VCF command

#317 yaseminbridges closed 3 months ago
0
add flag for `generate-stats-plot` for creation from TSV

#316 yaseminbridges closed 4 months ago
0
Add flag in `generate-stats-plot` to specify if plots are being created from TSV

#315 yaseminbridges closed 4 months ago
0
313 add option for hg19 and hg38 vcf for spiking command

#314 yaseminbridges closed 4 months ago
0
Add option for hg19 and hg38 VCF for spiking command

#313 yaseminbridges closed 4 months ago
0
311 implement a prepare corpus command

#312 yaseminbridges closed 4 months ago
3
Implement a `prepare-corpora` command

#311 yaseminbridges closed 4 months ago
2
307 add handling of chromosome naming in the phenopacket

#310 yaseminbridges closed 4 months ago
0
308 create pluginsmd

#309 yaseminbridges closed 4 months ago
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create plugins.md

#308 yaseminbridges closed 4 months ago
0
Add handling of chromosome naming in the phenopacket

#307 yaseminbridges closed 4 months ago
4
Implemented PhEval runners

#306 yaseminbridges closed 4 months ago
3
304 change matching of result files to phenopacket in benchmarking

#305 yaseminbridges closed 5 months ago
0
Change matching of result files to phenopacket in benchmarking

#304 yaseminbridges closed 5 months ago
0
302 add roc curves and precision recall curves to benchmarking output

#303 yaseminbridges closed 5 months ago
0