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Recent Releases of TMSig

TMSig - v1.1.1

BUG FIXES

  • cameraPR.matrix: data.table::setcolorder arguments before and after were added in data.table v1.15.0 (2024-01-30). Rather than requiring a recent minimum version of data.table, the code has been modified to no longer depend on these arguments.

Full Changelog: https://github.com/EMSL-Computing/TMSig/compare/v1.1.0...v1.1.1

- R
Published by TylerSagendorf about 2 years ago

TMSig - v1.1.0

What's Changed:

  • cameraPR.matrix: added alternative parameter to allow users to perform one-sided tests. A warning will be issued if attempting to use a one-sided test with the parametric version of CAMERA-PR, as this is generally not recommended.
  • cameraPR.matrix: added min.size parameter to allow users to specify a minimum set size for testing.
  • similarity and cluster_sets: added support for Ōtsuka set similarity.
  • Documentation for most functions has been updated.

Bugfixes:

  • cameraPR.matrix: fixed variance calculation when use.ranks=TRUE and inter.gene.cor=0.
  • enrichmap: fixed checks for duplicate contrast-set pairs.
  • enrichmap: if column or row labels are specified by the user through the heatmap_args parameter, the maximum text width or height is now determined from these new labels to avoid overlapping plot elements.
  • enrichmap: default of statistic_column parameter changed to "TwoSampleT" to match output of cameraPR.matrix.

Full Changelog: https://github.com/EMSL-Computing/TMSig/compare/v1.0.0...v1.1.0

- R
Published by TylerSagendorf about 2 years ago

TMSig - v1.0.0

  • Rename package from ostRich to TMSig: Tools for Analyzing Molecular Signatures.
  • Add fast cameraPR.matrix method based on limma::cameraPR.default. Add Di Wu and Gordon Smyth as contributors.
  • Add enrichmap function to generate bubble heatmaps of molecular signature analyses.
  • Update cluster_sets function to return a data.frame, rather than a data.table.
  • Rename prepare_gene_sets vignette to GO_analysis. Add example code for cameraPR.matrix.

Full Changelog: https://github.com/EMSL-Computing/TMSig/compare/v0.1.0...v1.0.0

- R
Published by TylerSagendorf about 2 years ago

TMSig - v1.0.0

  • Rename package from ostRich to TMSig: Tools for Analysis of Molecular Signatures.
  • Add fast cameraPR.matrix method based on limma::cameraPR.default. Add Di Wu and Gordon Smyth as contributors.
  • Add enrichmap function to generate bubble heatmaps of molecular signature analyses.
  • Update cluster_sets function to return a data.frame, rather than a data.table.
  • Rename prepare_gene_sets vignette to GO_analysis. Add example code for cameraPR.matrix.

Full Changelog: https://github.com/EMSL-Computing/TMSig/compare/v0.1.0...v1.0.0

- R
Published by TylerSagendorf about 2 years ago

TMSig - v0.1.0

Initial release.

Full Changelog: https://github.com/EMSL-Computing/ostRich/commits/v0.1.0

- R
Published by TylerSagendorf about 2 years ago