CimpleG

Description

DNA methylation signatures are usually based on multivariate approaches that require hundreds of sites for predictions. 'CimpleG' is a method for the detection of small CpG methylation signatures used for cell-type classification and deconvolution. 'CimpleG' is time efficient and performs as well as top performing methods for cell-type classification of blood cells and other somatic cells, while basing its prediction on a single DNA methylation site per cell type (but users can also select more sites if they so wish). Users can train cell type classifiers ('CimpleG' based, and others) and directly apply these in a deconvolution of cell mixes context. Altogether, 'CimpleG' provides a complete computational framework for the delineation of DNAm signatures and cellular deconvolution. For more details see Maié et al. (2023) <doi:10.1186/s13059-023-03000-0>.

Downloads

CRAN Check Status

Check History

Packages required but not available:
  'caret', 'parsnip', 'recipes', 'rsample', 'tune', 'workflows'

Packages suggested but not available for checking:
  'biomaRt', 'EpiDISH', 'minfi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

Package required but not available: ‘caret’

Package suggested but not available for checking: ‘EpiDISH’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

Package suggested but not available for checking: ‘EpiDISH’

Package suggested but not available for checking: ‘EpiDISH’

Dependency Network