NEWS.md

In genomaths/MethylIT: Methylation Analysis Based on Signal Detection

MethylIT 0.3.2.7

• Current version
• Actively used in methylome analysis
• In development
• 06-23-24
  • New functions added to identify DMRs and others accumulative improvements.

MethylIT 0.3.2.6

• Current version
• Actively used in methylome analysis
• In development

• 01-15-23:

  • Update function 'uniqueGRfilterByCov' adding parameter 'and.min.cov'. To get the results with previous default parameter set: and.min.cov = FALSE

• 02-07-23:

  • Add Random Forest algorithm to functions 'evaluateDIMPclass' and 'estimateCutPoint'.

MethylIT 0.3.2.5

• Current version
• Actively used in methylome analysis
• In development
• 05-12-22:
  • Add a new functions getDMGs wrapping several steps of DMG estimations.
  • Replace function 'data.table' with functions from dplyr package.

MethylIT 0.3.2.3

• Current version
• Actively used in methylome analysis
• In development
• 04-06-22:
  • Fixed issues with parallel computation.
• 11-04-21: 1) Upgrading corresponding to R version 4.1.1. - Improvement of parallel computation - Improvement on some non-linear algorithms.

MethylIT 0.3.2.2

• Actively used in methylome analysis
• In development
• 07-14-21: 1) Upgrading corresponding to R version 4.1.0. - Prevent potential crash originated by changes in some R packages internally used by Methyl-IT. - J-Divergence is now available in estimateCutPoint function

MethylIT 0.3.2.1

• Actively used in methylome analysis
• In development
• 06-09-20: 1) Upgrading corresponding to R version 4.0.0. - Prevent potential crash originated by changes in some R packages internally used by Methyl-IT.

MethylIT 0.3.2

• 04-17-20: 1) A new vignette added: - DMR detection with Methyl-IT
• 03-08-20: 1) Two new vignette added: - Principal Components and Linear Discriminant Analyses with Methyl-IT - Association Between Gene Expression and Cytosine DNA Methylation at gene-body
• 03-23-20: 1) Update documentation and code style reformatted

New features

• Improvement of the 'countTest' function applied for DMG identification. The new version was named 'countTest2'

• Added function 'gofReport' search for the best fitted model between the set of models requested by the user.

• The functions using machine-learning algorithms were improved

• The documentation was notably improved

MethylIT 0.3.1

• Available at https://git.psu.edu/genomath/MethylIT

MethylIT release

November 17, 2018: * Initial development.

genomaths/MethylIT documentation built on Feb. 3, 2024, 1:24 a.m.