Title: Multiple Logistic Regression for 3D Chromatin Domain Border
Depends: R (>= 3.2.0), GenomicRanges, Matrix, glmnet, rtracklayer
Description: We propose a multiple logistic regression model to assess the influences of genomic features such as DNA-binding proteins and functional elements on topological domain borders.

Title: Probing Factor-Dependent Long-Range Contacts using Regression
Description: We propose a generalized linear regression with higher-order interaction terms to assess the influences of genomic features such as DNA-binding proteins and functional elements on long-range contacts from Hi-C experiments.

Title: Hierarchical Climate Regionalization: An Improved Hierarchical
Clustering in R for Climate Regionalization
Maintainer: Hamada S. Badr <badr@jhu.edu>
Description: HiClimR package modifies and improves hierarchical clustering in R
('hclust' function in 'stats' library), for climate regionalization. It adds a new
clustering method (called, regional linkage) to the set of available methods together
with several features including regridding, coarsening spatial resolution, geographic
masking, data thresholds, detrending and standardization preprocessing, faster correlation
function, hybrid hierarchical clustering, and cluster validation.
Badr et. al (2014) describes the regionalization algorithms and data processing tools
included in the package and presents a demonstration application in which the package
is used to regionalize Africa on the basis of interannual precipitation variability.
It is applicable to any correlation-based clustering.
Badr, H. S., Zaitchik, B. F. and Dezfuli, A. K. (2014). An Improved Hierarchical Clustering
in R for Climate Regionalization. Journal of Statistical Software (JSS), Initial Submission.

Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Description: HiClimR package modifies and improves hierarchical clustering in R ('hclust' function in 'stats'
library), for climate regionalization. It adds a new clustering method (called, regional linkage)
to the set of available methods together with several features including regridding, coarsening
spatial resolution, geographic masking, data thresholds, detrending and standardization data
preprocessing, faster correlation function, hybrid hierarchical clustering, and cluster validation.