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al-folio

A beautiful, simple, clean, and responsive Jekyll theme for academics

aryeelab.dfci.harvard.edu

Aryee Lab Webpage

aryeelab.github.io-bak

Started 07June2017

baf_ews

bisulfite-seq-tools

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).

block_methylation

broad-epi-cut-n-run

Porting the 4d nucleosome Cut-and-Run pipeline to WDL

cas-designer

circleseq

cohesin_extrusion_reproducibility

Code repository to reproduce all results for Sept, et al. 2023

colon-dna-topology

crispr_mutation_reanalysis

Commands, scripts, and data for reanalysis of "Unexpected mutations after CRISPR–Cas9 editing in vivo"

cromwell-monitor

Generate stats for Cromwell task calls including resource utilization & estimated costs

diffloop

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.

diffloop-paper

Sample Analysis for diffloop paper

diffloopdata

An example dataset for the diffloop package

dnalandscaper

Shiny app that integrates ChIA-PET and other epigenetic tracks

dnalandscaper_tracks

Simple file showing the tracks in DNAlandscapeR

dnaloop

A preprocessing and QC pipeline for ChIA-PET data

encode-chip-seq-pipeline2

ENCODE ChIP-seq pipeline

encode-hic-pipeline

HiC uniform processing pipeline

erisone_dashboard

extrusion-sim

geomx-dnd

gm12878_hct116_targets

Analysis repo for targeting loops associated with GM12878 and HCT116

guideseq

Analysis pipeline for the GUIDE-seq assay.

guppy-cpu

guppy-gpu

hichipper

A preprocessing and QC pipeline for HiChIP data

hichipper-analyses

Repository for showing commands and reproducing hichipper analyses