coMethDMR - Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.

Last updated 5 months ago

dnamethylationepigeneticsmethylationarraydifferentialmethylationgenomewideassociation

6.47 score 7 stars 42 scripts 230 downloads

MethReg - Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.

Last updated 5 months ago

methylationarrayregressiongeneexpressionepigeneticsgenetargettranscription

5.45 score 5 stars 19 scripts 192 downloads

rnaEditr - Statistical analysis of RNA editing sites and hyper-editing regions

RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

Last updated 5 months ago

genetargetepigeneticsdimensionreductionfeatureextractionregressionsurvivalrnaseq

4.48 score 3 stars 9 scripts 242 downloads

ranktreeEnsemble - Ensemble Models of Rank-Based Trees with Extracted Decision Rules

Fast computing an ensemble of rank-based trees via boosting or random forest on binary and multi-class problems. It converts continuous gene expression profiles into ranked gene pairs, for which the variable importance indices are computed and adopted for dimension reduction. Decision rules can be extracted from trees.

Last updated 10 months ago

cpp

2.70 score 4 scripts 220 downloads