Collection of shell & R scripts used in the 2014 Methylation Analysis Workshop
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Updated
Dec 20, 2014 - R
Collection of shell & R scripts used in the 2014 Methylation Analysis Workshop
Performing a limited cluster for similar methylation profiles as SOX10
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.
Gaussian mixture modelling - Unsupervised learning
SCREW: A Reproducible Workflow for Single-Cell Epigenomics
Genomic Data Commons Query
Minimal methylation classifier (MIMIC): A novel method for derivation and rapid diagnostic detection of disease-associated DNA methylation signatures - We describe the development and validation of minimal methylation classifier (MIMIC), combining CpG signature design from genome-wide datasets, multiplex-PCR and detection by single-base extensio…
fastQTL analysis of methylation and expression data
Produces coverage and methylation percentage data from FASTQ files.
An application for analyzing and visualizing DNA methylation in multiple sequence alignments
cfDNA methylation probe design from mybaits targeted sequencing
This package creates segmentation of the genome into regions of biological significance from high-throughput sequencing data.
Important papers relating to the biology of cell free DNA
Using Snakemake to implement ENCODE WGBS pipeline
JBrowse plugin for methylation related things
EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.
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