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Simulation and analysis for a model coupling 3D chromatin structure and transcriptional dynamics

Module for assessing short simple repeats in either the context of variants (insertions/deletions) or a genome reference sequence.

Pre-processing scripts for DNMs from http://www.genemed.tech/gene4denovo/download - convert DNMs to BCF/VCF format for further analysis

Gauri's python scripts for mapping missense variants

Analysis of deletions in PCAWG ID4-positive tumours relative to TOP1-seq signal from Baranello et al. (2016): doi:10.1016/j.cell.2016.02.036

Genome wide analysis of emRiboSeq embedded ribonucleotide context preferences.

Pan-cancer analysis of deletion mutation patterns relative to genic transcription.

Configurable template for read alignment, processing and somatic variant calling using SGE cluster

Normalization and intersection of somatic variant calls from multiple callers

A public repo containing the scripts/config needed to interface with SOTR telemetry boxes etc.

CV for job

Temporary Test Project