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DIME (version 1.3.1)

Differential Identification using Mixture Ensemble

Description

A robust identification of differential binding sites method for analyzing ChIP-seq (Chromatin Immunoprecipitation Sequencing) comparing two samples that considers an ensemble of finite mixture models combined with a local false discovery rate (fdr) allowing for flexible modeling of data. Methods for Differential Identification using Mixture Ensemble (DIME) is described in: Taslim et al., (2011) .

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Version

Install

install.packages('DIME')

Monthly Downloads

324

Version

1.3.1

License

GPL (>= 2)

Maintainer

Cenny Taslim

Last Published

September 27th, 2026

Functions in DIME (1.3.1)

gng.qq.plot.internal

Internal function for QQ-plot of GNG model.
huber

Huber's weight function
nudge.classify

Classification Based on NUDGE Model
inudge.classify

Classification Based on iNUDGE Model
inudge.qq.plot.internal

Internal function for QQ-plot of iNUDGE model
inudge.fit

Function for Fitting iNUDGE model parameters
inudge.plot.mix

Plot iNUDGE Mixture Component Function
inudge.plot.qq

QQ-plot of GNG model vs. observed data
inudge.plot.comp

Plot iNUDGE Individual Components
inudge.plot.fit

Plot iNUDGE Goodness of Fit
nudge.fit

Function for Fitting NUDGE model parameters
nudge.plot.fit

Plot NUDGE Goodness of Fit
nudge.plot.comp

Plot NUDGE Individual Components
nudge.plot.qq

QQ-plot of GNG model vs. observed data
nudge.plot.mix

Plot NUDGE Mixture Component Function
gng.plot.comp

Plot GNG Individual Components
DIME.classify

Classification Based on The Best Model
DIME-package

DIME (Differential Identification using Mixtures Ensemble)
gng.classify

Classification Based on GNG Model
gng.fit

Function for Fitting GNG model parameters
DIME.plot.fit

Plot Best Model Goodness of Fit
gng.plot.fit

Plot GNG Goodness of Fit
gng.plot.mix

Plot GNG Mixture Component Function
DIME

DIME (Differential Identification using Mixtures Ensemble)
gng.plot.qq

QQ-plot of GNG model vs. observed data