Package: DIME 1.3.0

DIME: Differential Identification using Mixture Ensemble

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) <doi:10.1093/bioinformatics/btr165>.

Authors:Cenny Taslim <[email protected]>, with contributions from Dustin Potter, Abbasali Khalili and Shili Lin <[email protected]>.

DIME_1.3.0.tar.gz
DIME_1.3.0.zip(r-4.7)DIME_1.3.0.zip(r-4.6)DIME_1.3.0.zip(r-4.5)
DIME_1.3.0.tgz(r-4.6-x86_64)DIME_1.3.0.tgz(r-4.6-arm64)DIME_1.3.0.tgz(r-4.5-x86_64)DIME_1.3.0.tgz(r-4.5-arm64)
DIME_1.3.0.tar.gz(r-4.7-arm64)DIME_1.3.0.tar.gz(r-4.7-x86_64)DIME_1.3.0.tar.gz(r-4.6-arm64)DIME_1.3.0.tar.gz(r-4.6-x86_64)
DIME_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DIME/json (API)

# Install 'DIME' in R:

install.packages('DIME', repos = c('https://olechnwin.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.63 score 43 scripts 223 downloads 19 mentions 24 exports 0 dependencies

Last updated from:4c34813ded. Checks:11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	106
linux-devel-x86_64	NOTE	87
source / vignettes	OK	143
linux-release-arm64	NOTE	96
linux-release-x86_64	NOTE	108
macos-release-arm64	NOTE	140
macos-release-x86_64	NOTE	209
macos-oldrel-arm64	NOTE	212
macos-oldrel-x86_64	NOTE	304
windows-devel	NOTE	78
windows-release	NOTE	90
windows-oldrel	NOTE	76
wasm-release	OK	86

Exports:DIME DIME.classify DIME.plot.fit gng.classify gng.fit gng.plot.comp gng.plot.fit gng.plot.mix gng.plot.qq gng.qq.plot.internal huber inudge.classify inudge.fit inudge.plot.comp inudge.plot.fit inudge.plot.mix inudge.plot.qq inudge.qq.plot.internal nudge.classify nudge.fit nudge.plot.comp nudge.plot.fit nudge.plot.mix nudge.plot.qq

Dependencies:

Help page	Topics
DIME (Differential Identification using Mixtures Ensemble)	DIME.package DIME_package
DIME (Differential Identification using Mixtures Ensemble)	DIME
Classification Based on The Best Model	DIME.classify
Plot Best Model Goodness of Fit	DIME.plot DIME.plot.fit
Classification Based on GNG Model	gng.classify
Function for Fitting GNG model parameters	gng.fit
Plot GNG Individual Components	gng.plot.comp
Plot GNG Goodness of Fit	gng.plot.fit
Plot GNG Mixture Component Function	gng.plot.mix
QQ-plot of GNG model vs. observed data	gng.plot.qq
Huber's weight function	huber
Classification Based on iNUDGE Model	inudge.classify
Function for Fitting iNUDGE model parameters	inudge.fit
Plot iNUDGE Individual Components	inudge.plot.comp
Plot iNUDGE Goodness of Fit	inudge.plot.fit
Plot iNUDGE Mixture Component Function	inudge.plot.mix
QQ-plot of GNG model vs. observed data	inudge.plot.qq
Classification Based on NUDGE Model	nudge.classify
Function for Fitting NUDGE model parameters	nudge.fit
Plot NUDGE Individual Components	nudge.plot.comp
Plot NUDGE Goodness of Fit	nudge.plot.fit
Plot NUDGE Mixture Component Function	nudge.plot.mix
QQ-plot of GNG model vs. observed data	nudge.plot.qq

Package: DIME 1.3.0

DIME: Differential Identification using Mixture Ensemble

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)