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npdro

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Nearest-neighbor Projected Distance Regression - Optimized (npdro). npdro extends ndpr feature selection by optimizing neighborhoods and the number of neighbors to detect main effects and interactions in high-dimensional datasets. Neighbor optimization methods include consensus nested cross-validation (cncv) with classification, varible-wise optimized-k (vwok), and principal component optimized-k (kPCA). npdro also includes optional speed optimizations.

Websites

NPDR Github Page

insilico Github Organization

insilico McKinney Lab

Related References.

2020 NDPR paper in Bioinformatics

2013 Gene-Wise Adaptive-Neighbors paper in PLoS One

To install:

>library(devtools)

>install_github("insilico/npdro")  
>library(npdro)

Dependencies

To install the tidyverse collection of R packages:

install.packages('tidyverse')

To set fast.reg = TRUE or fast.dist = TRUE or use.glmnet = TRUE, please install the speedglm and glmnet packages:

install.packages(c('speedglm', 'wordspace', 'glmnet'))

If an issue arises with updating openssl, try updating it on your own system, e.g. for MacOS:

brew install openssl@1.1

Examples

Abstract

Contact

brett.mckinney@gmail.com

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