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gcap 1.1.4

  • Removed the XGBOOST version limits, instead, a warning is posted.
  • Used GitHub action to render pkgdown site.

gcap 1.1.3

  • Updated the logic of using only_oncogenes for filtering.

gcap 1.1.2

  • Fixed the data loading for oncogene of mouse.

gcap 1.1.1

  • Updated Sequenza workflow.
  • Fixed the re-handling of errored seqz and facets runs.

gcap 1.1.0

  • Supported analysis workflow from FACETS and Sequenza.
  • Mouse genome is enabled based on the two implemented workflows above.

gcap 1.0.0

  • The first public and stable release.

gcap 0.21.0

gcap 0.20.2

  • Limited xgboost version lower than 1.6 as it will not keep some key info in .rds file.

gcap 0.20.1

  • Enhance the getGeneSummary() and getCytobandSummary() methods to return mutation matrix.

gcap 0.20.0

  • This version is not compatible with previous versions, as the analysis and visualization functions are moved to an independent package 'gcaputils'.

gcap 0.14

  • Added some utils functions and visualization functions.

gcap 0.13

  • Updated initial setting and CLI.

gcap 0.12

This version has been discarded from git history.

gcap 0.11.1

  • Supported a NA passing as tightness to remove the use of TCGA blood summary data as a more strict threshold for circular amplicon.

gcap 0.11.0

  • Added fCNA$subset() method.
  • Added gcap.plotDistribution() function.

gcap 0.10.0

  • Added gcap.plotForest().
  • Added gcap.plotKMcurve().
  • Added gcap.plotProfile().
  • Added method convertGeneID() to fCNA class.
  • Set a default value for pdata option in fCNA$new().

gcap 0.9.0

  • Supported gcap as main command, and previous two commands as subcommands if GetoptLong version >=1.1.0. Note: not test yet.

gcap 0.8.1

  • Cleaned logic.

gcap 0.8.0

  • Added options tightness and gap_cn.
  • Renamed gcap-wes.R script to gcap-bam.R.

gcap 0.7.0

  • Handled void result.
  • Updated the background copy number reference and criterion judging a amplicon (#22).

gcap 0.6.0

  • Designed and implemented a class fCNA used for storing the workflow key outputs and downstream analysis and visualization.

gcap 0.5.0

  • Provided a function convertID() to convert gene IDs.
  • Optimized the output summary.
  • Re-constructed scoring and workflow output.

gcap 0.4.1

  • Added use_best_ntreelimit in gcap.runPrediction() to control the ntree setting. When it is FALSE, we use a custom processing to obtain a more conservative tree number.
  • Added deploy() to auto-deploy the CLI to /usr/loca/bin.
  • Added easy-to-use CLI in inst directory.
  • Filled NAs to input when age and gender are not available.
  • Automatically appended logs to specific directory with rappdirs::app_dir("gcap", "ShixiangWang"). Users can obtain log path and cat log info with gcap:::get_log_file() and gcap:::cat_log_file() for debugging. (#14)
  • Supported XGB54 model in workflows. (#13)

gcap 0.4.0

  • After exploration, we found our stepwise model outperform MBO tuned model. So the models for predicting circular target have been limited to 3.
  • gcap.ASCNworkflow() now supports input with only total integer copy number, like the result from ABSOLUTE software (also DoAbsolute).
  • Added stepwised model for circle target.
  • Changed the way how to select model and run prediction.
  • custom_model in gcap.runPrediction() has been changed to model. This is inconsistent with version below v0.4.

gcap 0.3.3

  • Updated scoring for supporting different thresholds.
  • Wrapped ASCAT workflow in tryCatch() to avoid abnormal failure.

gcap 0.3.2

  • Fixed input extra_info sample (order) issues.

gcap 0.3.1

  • Fixed the issue about rendering wrong data files when skipping existing ASCAT calling.

gcap 0.3.0

  • Updated models for prediction.

gcap 0.2.1

  • Removed prob_cutoff setting in workflows. Directly use prob 0.1, 0.5 and 0.9 for cutting low, medium and high quality amplicon.

gcap 0.2.0

  • Implemented an alternative workflow from allele specific copy number data to final result files. (#5)

gcap 0.1.0

  • Implemented basic workflow from BAM files to result files.
  • Added a NEWS.md file to track changes to the package.