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Suite of tools to conduct methylation data analysis. Methods from this workspace can be used for alignment and quality control analysis for various protocols including Whole Genom Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS) and Hybrid Selection Bisulfite Sequencing (HSBS).
A preprocessing and QC pipeline for HiChIP data
Processing pipelines for HiC and other 3D genome tools
Analysis pipeline for the GUIDE-seq assay. For news, see:
Aryee Lab Webpage
R package for the efficient compression of HiC data
Reference for Lab Members + Quick Start Guide for New Additions
Analysis repo for targeting loops associated with GM12878 and HCT116
Preprocessing tools for unique molecular index (UMI) sequencing reads
Commands, scripts, and data for reanalysis of "Unexpected mutations after CRISPR–Cas9 editing in vivo"
Shiny app that integrates ChIA-PET and other epigenetic tracks
Sample Analysis for diffloop paper
Repository for showing commands and reproducing hichipper analyses
Simple file showing the tracks in DNAlandscapeR
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/diffloop.html Contributions: https://github.com/aryeelab/diffloop. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=diffloop or https://github.com/aryeelab/diffloop/issues.
Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
Data repository of HiC experiments processed through different preprocessing pipelines
An example dataset for the diffloop package
Martin's misc R utility functions
A preprocessing and QC pipeline for ChIA-PET data
Devel repository for minfi
Most used topics
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