Comments (5)
Was wondering if I did something wrong with the no-docker install, checked the Dockerfile changes in the new release, and there are a lot of them sigven/pcgr@821102f#diff-28b3886804b6c975a958b69b941ea9af
Is it possible by any chance to make a summary of dependencies changes? :)
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To address the original bug, had to move the file data-raw/data-raw.R
into R/
, and add line
export(acmg_evidence_codes)
into the NAMESPACE
file
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Vlad,
Thanks a lot for this. Pretty much relying on you for the no-docker part:-) Will try to see if i can make a summary of the dependencies.
best,
Sigve
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If you are still doing some stuff in the grch37 world, take a note of this:
Ensembl/ensembl-vep#413
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Wow, missing annotations on entire chromosome is huge. But that's only for dbSNP and gnomAD? Shouldn't be a problem for us, we annotate with those separately and we don't use tumor-only filtering in PCGR. But yeah, in UMCCR we are still doing GRCh37 for some unknown reason
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Related Issues (20)
- ERROR while running HOT 3
- cpsr_validate_input.py: error: argument vcf_validation: invalid int value: '/home/zdjzyx01/biosoft/cpsr/cpsr.toml' HOT 11
- Missed variant due to transcript pick? HOT 9
- cpsr_configuration_default.toml missing from PCGR data HOT 2
- Error: Problem with `mutate()` input `ACMG_PVS1_1`. HOT 4
- Error in loadNamespace(name) : there is no package called 'reactable' HOT 2
- x object 'GWAS_CITATION' not found HOT 3
- ImportError: No module named toml HOT 1
- minor typo in src/cpsr_functions.R HOT 1
- Error: `x` and `y` must share the same src HOT 5
- genes being excluded from CPSR exploratory track HOT 5
- Not able to download the data bundles (404 Error) HOT 2
- ACMG guideline updated to version 3.0. New genes were added to the secondary finding gene list. HOT 2
- make infromation like ckb to cpsr HOT 4
- Encounter the error in cpsr-report-generation() HOT 3
- Installation Instructions Only Describe Conda HOT 2
- Add sif file for running on an HPC HOT 1
- Biomarker variants not in Pathogenic/Likely Pathogenic section of report HOT 1
- adding clones IDs + child clone emerging outside parent clone HOT 2
- Feature Request - support CNV calls (and ideally SV calls) HOT 5
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