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alphafold

Open source code for AlphaFold.

alphamissense

data_analysis_with_python-coursework

data analysis with python

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

ega_data_submission

Describe steps of data submission to EGA database

ffpesig

Codes and Data for FFPEsig manuscript

gpt-pilot

Dev tool that writes scalable apps from scratch while the developer oversees the implementation

hmftools

Various algorithms for analysing genomics data

iods-coursework

template for IODS course projects

machinelearning_molecularbiology-coursework

All you need to know about mutational sigs

nanogpt

The simplest, fastest repository for training/finetuning medium-sized GPTs.

phasetank

This repository mirrors the tool (PhaseTank) I developed during my MSc

shallowsig

Our method for detecting mutational patterns in shallow sequencing data

sigprofilermatrixgenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

software_installation

This repo will record instructions for software installation on the current cluster I am working on

tumouronly_mutsig

Identifying mutational signatures in deep and shallow tumour only samples

vcf-liftover

Liftover VCF files

ydata-profiling

1 Line of code data quality profiling & exploratory data analysis for Pandas and Spark DataFrames.