Analysis Pipeline for Single Cell ATAC-seq
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Updated
Apr 27, 2023 - R
Analysis Pipeline for Single Cell ATAC-seq
🎯 ChIP peak Annotation, Comparison and Visualization
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Modelling DNA methylation profiles
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
Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
Bacterial Epigenomics Analysis SuiTe
R/Bioconductor package for optimized functional annotation of ChIP-seq data
Calculate DNA methylation age using Horvath 2013 method
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.
Differential Epigenetic Correlation Test
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
Online version of tool is live
For inferring ancestry, gestational age, and cell type proportions from placental DNA methylation array data
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)
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.
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.
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