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Commits on Mar 25, 2025

• correct README typo

  andreadega

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  0e6b9f5

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• changed version to 2.4.6

  andreadega

  committed
  b5bf680

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• testing genomeChartSV and plotJunctionCatalogue

  andreadega

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  515a215

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• Junction catalogue update to remove imprecise variants and return the count of imprecise variants along with it

  andreadega

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  c58fe21

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• added the plotRegion function

  andreadega

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  88e0cd2

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Commits on Feb 2, 2025

• updated genomeChartSV function

  andreadega

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  48b173b

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Commits on Jan 19, 2025

• update improvement to assign signature probability to mutations

  andreadega

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Commits on Nov 18, 2024

• added function to find context of SNVs and plot the results

  andreadega

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Commits on Nov 15, 2024

• updated version in description file

  andreadega

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  d84b68a

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Commits on Oct 16, 2024

• added HRDetect option to set rare candidate selection criteria, and default to MinError

  andreadega

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Commits on Jul 2, 2024

• added option to allow for unassigned mutations in the assignSignatureProbabilityToMutations function

  andreadega

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Commits on Jun 13, 2024

• change version to v2.4.5

  andreadega

  committed
  9e2ef8d

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• making GenSA dependency optional

  andreadega

  committed
  4c146ae

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• added odd ratio with confidence interval for single sample strand bias and corresponding plot

  andreadega

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  49ea55e

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Commits on May 21, 2024

• fixed calculation of percentage of mutations when using bootstrap in legacy code

  andreadega

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  2246efa

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Commits on Apr 12, 2024

• fixed test for the assignSignatureProbabilityToMutations function

  andreadega

  committed
  f8f6cbf

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Commits on Mar 7, 2024

• improvements to indels and rearrangements classification to account for some exceptional cases

  andreadega

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Commits on Feb 13, 2024

• allow empty catalogues to run with signature fit with bootstrap

  andreadega

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Commits on Jan 29, 2024

• documentation correction for command line scripts

  andreadega

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  c276bec

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Commits on Jan 26, 2024

• fixed missing rareCandidateSelectionCriteria parameter in FitMS call when running singatureFit_pipeline

  andreadega

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Commits on Jan 25, 2024

• added two aggregation plots for plotFit and plotFitMS

  andreadega

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Commits on Jan 22, 2024

• fixed bug with solution selection for FitMS command line script

  andreadega

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  169f89d

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Commits on Jan 17, 2024

• genomeChart and plotCopyNumbers support for mm10 and canFam3. Added option -A in genomeChart script to save annotated mutations as plain text tables

  andreadega

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Commits on Jan 8, 2024

• fix to README anchor

  andreadega

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  45a5510

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Commits on Jan 5, 2024

• fix missing initialised variable introduced in previous commit

  andreadega

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  59a3a32

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• HRDetect with bootstrap now returns a pvalue, also change to v2.4.4

  andreadega

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  0ae4567

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• added standard error combined strand bias plots

  andreadega

  committed
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Commits on Jan 3, 2024

• added strandBias test and added more stats in the combined result

  andreadega

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  b989754

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• added assignSignatureProb NaN check, and test

  andreadega

  committed
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Commits on Jan 2, 2024

• fixed plotMatrix error if all elements in the matrix are NA

  andreadega

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• prevent running bootstraps if one of the catalogues contains less than one mutations

  andreadega

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  b26066b

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Commits on Oct 27, 2023

• bedpeToRearrCatalogue fix in case all SVs are shorter than 1kb

  andreadega

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Commits on Oct 25, 2023

• Merge branch 'master' into dev

  andreadega

  committed
  f9c1630

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• Merge pull request #56 from Nik-Zainal-Group/dockerfile

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  andreadega

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  7ab0aac

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• Updated Dockerfile.

  janczarn

  committed
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