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PALMER: A Constrained Biclustering Algorithm to Improve Pathway Annotation Based on the Biomedical Literature Mining
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README.md

PALMER

PALMER (a constrained biclustering algorithm to improve Pathway Annotation based on the biomedical Literature Mining) is a constrained biclustering approach that allows to identify indirect relationships among genes based on the text mining of biomedical literature, which allows researchers to utilize prior biological knowledge to guide identification of gene-gene associations. 'palmer' package provides computationally efficient and user friendly interface to fit the PALMER models. The 'palmer' vignette provides a good start point for the step-by-step data analysis using 'palmer' package.The following help pages provide a good start point for the genetic analysis using the 'GPA' package, including the overview of 'GPA' package and the example command lines:

library(palmer)
package?palmer
class?palmer
vignette("palmer")

Installation

The stable versions of 'palmer' package can be obtained from the following URLs:

Package source: https://github.com/dongjunchung/chunglab_binary_packages/blob/master/palmer_0.1.tar.gz

Windows binary: https://github.com/dongjunchung/chunglab_binary_packages/blob/master/palmer_0.1.zip

Mac OS/X binary: comming soon

To install the developmental versions of 'palmer' package, it's easiest to use the 'devtools' package.

#install.packages("devtools")
library(devtools)
install_github("dongjunchung/palmer", build_vignettes= TRUE)

References

Nam JH, Couch D, Silveira W.A, Yu Z and Chung D (2019) ''PALMER: A constrained biclustering Algorithm to improve pathway annotation based on the biomedical literature mining''.

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