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We aim to share our outputs with the scientific community and have developed a range of open source tools.

 

                                 

Description

Group

CapSequm.png

CapSequm

Online tool to design oligonucleotides for multiple targets for use in next generation (NG) Capture-C experiments. Reference

Hughes, Taylor

CGAT.jpg

Computational Genomics Analysis Toolkit

Sims
csynth_logo.png

CSynth

CSynth is a physics based interactive visualisation platform for visualizing the 3D structure of the biological molecules. It is primarily designed to provide an engaging way to explore and understand the complex structure of the genome in 3D by integrating data from next generation sequencing (Hi-C) and modelling. For example, it allows the user to see a traditional Hi-C heat map overlaid with dynamically generated or precomputed 3D structures. Reference

Taylor
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HEM Database

The Human Erythroblast Maturation database (HEM) contains differentially regulated and continuously expressed transcripts: a resource for future functional studies of erythropoiesis.

Taylor
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LanceOtron

A graphical tool for peak calling chromatin profiling assays e.g. ChIPseq. LanceOtron utilises a powerful computer vision, deep learning algorithm to analyse the shape of peaks. Initial parameters can be selected interactivly and the final results further refined by the help of charts and images.

Taylor, Hughes,

MIG

The Multi-Image Genome viewer (MIG) is primarily aimed at high-throughput sequencing experiments where a "signal" is detected at multiple locations across the genome (such as ChIP-Seq and RNA-Seq). MIG allows the user to filter, sort and visualise these regions of interest in their local genome context. Reference

Taylor
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miR-CRISPR

The miR-CRISPR tool is an integrated algorithm designed to facilitate CRISPR / Cas9 genome engineering of putative microRNA response elements (MREs). Reference

Taylor
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MLV

MLV (Multi Locus View) has been developed to allow users to fluidly interact with genomics datasets at multiple scales, from complete metadata labelled and clustered populations to detailed representations of individual elements. It has inbuilt tools to integrate signals across multiple dataset and to perform dimensionality reduction and clustering analysis.

[bioRxivGitHub]

Taylor, Hughes

Ruffus

A pipelining tool for Python

Sims
SasQ_logo.png

Sasquatch

Predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints. Reference

Hughes

 

UMI-tools

Deduplication using molecular barcodes

Sims
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WMD

Comparison of reference and mutant DNA: identifies restriction enzymes that cut the two sequences in a discriminative manner

Taylor
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Zegami

Zegami lets you search, sort, filter and group collections of images in real time and in a single field of view. It allows you to load not only your images, but also the associated metadata and has an array of in-built filters that make it easy to see patterns and identify relationships based on the data contained in each image.

Taylor