R package for DNA methylation analysis
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Updated
Jan 22, 2024 - R
R package for DNA methylation analysis
SCREW: A Reproducible Workflow for Single-Cell Epigenomics
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
A Snakemake pipeline for RRBS data analysis
Bioinformatics Pipeline
Bayesian Clustering and Imputation of Single Cell Methylomes
Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
DISMISS is an R script, which as an additional step in MeDIP-Seq data analysis workflow, enables the allocation of strands to methylated DNA regions. It does this by analyzing the proportions of first mate reads aligning to the methylated locus from the plus and minus strands.
A tool for discovering Differentially Methylated Regions
Bacterial Epigenomics Analysis SuiTe
Gaussian mixture modelling - Unsupervised learning
A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing
The package msap provides a easy way to analyse MSAP (Methylation-Sensible Amplified Polymorphism) data in order to asses epigenetic and genetic differences between groups of samples.
Whole-Genome Inherited Bisulphite Sequencing Data Simulation
Correction of batch effects in DNA methylation data
GuidingNet is a method to reveal transcriptional cofactor and predict binding for DNA methyltransferase by network regularization.
Methylation Array Cross-Reactive Probes
CytoMeth tool compiles a set of open source software named in the Roche pipeline guidelines to perform SeqCap Epi data analysis.
A public repo to share methylation risk scores (MRS) derived from UCLA's electronic health records.
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