Title: EWAS using reference-Free DNA methylation mixture deconvolution
Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types.  This method is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.

Title: EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types.
The older method (Houseman et al., 2014) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.
The newer method (Houseman et al., 2016) is similar to non-negative matrix factorization, with additional constraints and additional utilities.

The older method (Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.
The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factorization, with additional constraints and additional utilities.

Reference-free method for conducting EWAS while deconvoluting DNA methylation
arising as mixtures of cell types.  The older method
(Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to
surrogate variable analysis (SVA and ISVA), except that it makes additional use
The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar
to non-negative matrix factorization, with additional constraints
Packaged: 2018-12-14 05:31:13 UTC; EHouseman

Package: RefManageR
Version: 0.10.12
Date: 2016-03-26
Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Authors@R: person(c("Mathew", "W."), "McLean", role = c("aut", "cre"),
email = "mathew.w.mclean@gmail.com")
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Description: Provides tools for importing and working with
bibliographic references.  It greatly enhances the 'bibentry' class by
providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references,
supports 'UTF-8' encoding, and can be easily searched by any field, by date
ranges, and by various formats for name lists (author by last names,
translator by full names, etc.). Entries can be updated, combined, sorted,
printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files
can be read into 'R' and converted to 'BibEntry' objects.  Interfaces to 'NCBI Entrez',
'CrossRef', and 'Zotero' are provided for importing references and
references can be created from locally stored 'PDF' files using 'Poppler'.  Includes
functions for citing and generating a bibliography with hyperlinks for
documents prepared with 'RMarkdown' or 'RHTML'.
License: GPL-2 | GPL-3 | BSD_3_clause + file LICENSE
Imports: XML, RCurl, RJSONIO, utils, plyr, tools, httr, bibtex,
lubridate (>= 1.5.0), stringr, methods
Suggests: knitr, testthat
Encoding: UTF-8
Depends: R (>= 3.0)
VignetteBuilder: knitr
BugReports: https://github.com/mwmclean/RefManageR/issues
NeedsCompilation: no
Packaged: 2016-03-31 18:57:27 UTC; mwm
Repository: CRAN
Date/Publication: 2016-03-31 22:27:35