Predicting Tissue Specific Enhancer Activity from Epigenetic Marks and Sequence
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Updated
Dec 3, 2014 - Python
Predicting Tissue Specific Enhancer Activity from Epigenetic Marks and Sequence
The documented analysis of the results reported in Akol et al., 2023 as R markdowns, Galaxy histories and jupyter logs..
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
Ultralight and fast implementation of GoPeaks to call peaks in CUT&Tag/CUT&RUN data
[ACM-BCB 2023 Oral Presentation] Official repository of "Deep learning-based survival prediction using DNA methylation-derived 3D genomic information"
This repo contains python scripts used in Mack et al. 2022 (doi.org/10.1016/j.jmb.2022.167482). This includes MD simulations code and analysis scripts. The usage of these Python scripts is further explained in the enclosed README.pdf
Github Page for the Baccarelli Lab
Code for "Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity"
A collection of simple scripts to facilitate the setup of everyday epigenetics experiments and to handle genomic methylation data
DecoFlex deconvolution method for Omic data implemented as DecoFlexR
Produces coverage and methylation percentage data from FASTQ files.
This repository contains methylation AFLP data as employed in Rodríguez-Casariego et al., Frontiers in Marine Sciences, 2020: "Genome-wide DNA methylation analysis reveals a conserved epigenetic response to seasonal environmental variation in the staghorn coral Acropora cervicornis"
Snakemake workflow for processing small RNA-seq libaries
CutNtag pipeline for Pasini's lab written in snakemake
Interactive Visualization Browser for Transposable Elements (TEs) community
Tools for epigenetic data analysis
Python code to control my physical model of an Epigenetic Landscape.
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