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Commits on Dec 30, 2024

• Many new classes for comparing Kohli CNV and GATK datasets.

  

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Commits on Jul 26, 2024

• New app to convert cBioPortal mutation table output to vcf format.

  

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Commits on Jul 9, 2024

• Build out the z-score normalization gene selection method for Copy

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Commits on Jun 28, 2024

• Near final modifications for the integrated KEGG MEDICUS pathway

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Commits on Jun 22, 2024

• Major effort to unify pathway analysis using KEGG MEDICUS for variant

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Commits on May 28, 2024

• Several modifications to support single line billing summaries for the

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Commits on Apr 8, 2024

• Rebuild of the billing process. Updates to the TNRunner run, qc, and

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Commits on Dec 27, 2023

• New apps for working with Invitae bulk results processing and GNomEx

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Commits on Sep 11, 2023

• Modifications to several apps for searching the PMR, running TNRunner,

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Commits on Jul 17, 2023

• Lots of misc changes, no major bug fixes, new app for CBI billing

  

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Commits on Apr 18, 2023

• Adding ability to print out all the clinical and report attribute info

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Commits on Apr 10, 2023

• Adding beta version of a tool for searching the patient molecular

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Commits on Dec 16, 2022

• Updated the SubjectMatchmaker in the USeq package to use the longer IDs.

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Commits on Nov 23, 2022

• Refactored so it generates an empty output file when no regions are

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Commits on Nov 22, 2022

• Made mods to filter and flag variant calls from Strelka GATK joint

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Commits on Nov 12, 2022

• New application for detecting copy ratio changes in cfDNA samples. Major

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Commits on Oct 10, 2022

• Added additional stats re copy ratio intersection with LoH regions

  

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Commits on Oct 9, 2022

• Added CopyRatio intersection function to LoH app.

  

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Commits on Oct 7, 2022

• Finalization of LoH, fixed issue with depreciate SamHeader

  

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• Added in INDEL variant scoring into the LoH app.

  

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• Adding new app, LoH, for finding loss of heterozygosity germline

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Commits on Sep 27, 2022

• New application for processing Avatar datasets independantly of the

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Commits on Aug 12, 2022

• Modifications to the Tempus data wrangler and TNRunner2 apps to enable

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Commits on Jun 14, 2022

• Lots of modifications to the Caris and Tempus processing apps.

  

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Commits on Apr 5, 2022

• Updates to the Tempus Json parser to accomodate 1.4.2. New app for

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Commits on Mar 15, 2022

• Fixed issue with the AnnotatedVcfParser not placing all gene names into

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Commits on Mar 14, 2022

• Fixed issue where exits didn't show failed state.

  

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Commits on Mar 10, 2022

• Further dev of Caris dataset processing and the VariantPathwayComparator

  

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Commits on Mar 1, 2022

• Adding new app for pathway analysis with somatic variants

  

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Commits on Feb 14, 2022

• Addition of a reworked AggregateQCStats2 app to match with the reworked

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Commits on Jan 13, 2022

• Fixed issue with the clinvar file date not appearing in the summary

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Commits on Dec 16, 2021

• Minor modifications for method compatibility

  

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Commits on Nov 10, 2021

• Improvements to TNRunner2 to utilize Illumina 10 batch germline variant

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Commits on Oct 7, 2021

• Minor changes to the old TNRunner to accomodate the new TNRunner2

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Commits on Oct 6, 2021

• Additional changes for TNRunner2

  

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