Efficient visualizations for DNA methylation data
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Updated
Nov 16, 2020 - R
Efficient visualizations for DNA methylation data
Supplemental codes for the Chapter 14 Chromatin Sequencing and Data Analysis of the NYMU-GRC eBook 基因體技術與資料分析手冊
DecoFlex deconvolution method for Omic data implemented as DecoFlexR
Code for the crb2a multi omics manuscript
This pipeline is designed for the analysis of DNA methylation data generated from the Illumina HumanMethylation450 BeadChip platform.
Code accompanying the findings in Duran-Ferrer 2020, Nat Cancer. The epiCMIT mitotic clock calculator and a Pan B-cell tumor classifier algorithm are provided.
A gene regulation model reveals an ancestral adaptation response to particulate exposure triggered by nanomaterials
Analysis of Single Molecule Footprinting (SMF) data for the analysis of DNA methylation, chromatin accessibility and TF binding. The repository contains all primary code to reproduce the main analyses for the publication "Single molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation" (Kreibich et al., 2023)
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.
scripts for scRNA-Seq/scATAC-Seq
After getting the bed file from the Peak calling, we can annotate and create all downstream analysis of two sets of data
SMP: A Salmonella Methylation analysis Pipeline
Provides easy to use, objective oriented functions for preprocessing methylation data produced by an Illumina Infinium BeadChip and detecting differentially methylated positions and regions within the DNA.
Repository containing the scripts and the analysis plan from "Pre-pregnancy maternal body mass index and placental DNA methylation: a meta-analysis of 2,631 mother-child pairs" by N. Fernandez-Jimenez et al (under review in Commun Biol).
Identification of epigenetic sites in MealyBugs using ONT Nanopore Sequencing
Online version of tool is live
Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"
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