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Hughes-Genome-Group

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deepC

A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence

deepHaem

Implementation of a deep convolutional neural network for predicting chromatin features from DNA sequence

NGseqBasic

Mapping, filtering, and data hub visualisation pipeline for DNase, ATAC, ChIP data

sasquatch

Predicting the impact of regulatory SNPs from cell and tissue specific DNase-footprints

Downes_2021_LZTFL1_Covid

Custom codes for data analysis.

mlv

CCseqBasicS

CCseqBasic - stable version of CCseqBasic analysis pipeline (getting updates when dev pipeline features get stable enough)

zegamiutils

Utility methods for Zegami

captureC

CaptureC analysis code by James Davies - to serve as supplements to the publication.

CCseqBasicF

CCseqBasic - freeze version with CF3 CF4 CF5 run modes (to run with different duplicate filtering options)