smsinks
A computational biologist with broad research interests that lie at the intersection of molecular medicine, data science and machine learning.
Cape Town
Pinned Repositories
Analysis-of-Cancer-Gene-Mutations
Mutation Landscape of Cancer-Driver Genes Across Human Cancers
COVID-19-Prediction-in-Africa-using-SIR-Model
DREAM-Preterm-Birth-Prediction-Challenge-Transcriptomics-Sinkala
MATLAB code for making predictions for the DREAM Preterm Birth Prediction: see https://www.synapse.org/#!Synapse:syn18380862/wiki/ for details
epigenetic-gene-variant-dynamics-analysis
This repository contains the analysis pipeline and scripts for the study "Mapping Epigenetic Gene Variant Dynamics: Comparative Analysis of Frequency, Functional Impact, and Trait Associations in African and European Populations." It includes custom code for data processing, statistical analysis, and visualisation.
Integrated-Analysis-of-MAPK-Pathway-Across-Human-Cancers
InterpretableModels.jl
Interpretable and Explainable AI/Machine Learning
Pancancer-Metabolic-Gene-Alterations
Metabolic Gene Alterations Across 32 Cancer Types and Their Clinical Significance
Single-Cell-Signaling-in-Breast-Cancer-Challenge
Scripts for the Single Cell Signalling in Breast Cancer - DREAM Challenge
smsinks's Repositories
smsinks/Analysis-of-Cancer-Gene-Mutations
Mutation Landscape of Cancer-Driver Genes Across Human Cancers
smsinks/epigenetic-gene-variant-dynamics-analysis
This repository contains the analysis pipeline and scripts for the study "Mapping Epigenetic Gene Variant Dynamics: Comparative Analysis of Frequency, Functional Impact, and Trait Associations in African and European Populations." It includes custom code for data processing, statistical analysis, and visualisation.
smsinks/bacterial_wgs_bioinformatics
This training focuses on characterizing the whole genome sequences of Enterobacterales and Pseudomonas to improve diagnostics, develop targeted therapies, and enhance the understanding and control of the potentially harmful bacteria.
smsinks/Bayesian-spatial-PSM
Bayesian spatial propensity score matching
smsinks/biomarkers
Genetics of blood and urine biomarkers in the UK Biobank
smsinks/CMplot
📊 Circular and Rectangular Manhattan Plot
smsinks/ComfyUI_VisualStylePrompting
ComfyUI Version of "Visual Style Prompting with Swapping Self-Attention"
smsinks/course-content
Summer course content for Neuromatch Academy
smsinks/course-content-dl
smsinks/dndscv
dN/dS methods to quantify selection in cancer and somatic evolution
smsinks/ECLIPSER
Enrichment of Causal Loci and Identification of Pathogenic cells in Single Cell Expression and Regulation data
smsinks/Evolution
Code accompanying The Evolutionary history of 2,658 cancers
smsinks/Explicit-Visual-Prompt
[CVPR 2023] Explicit Visual Prompting for Low-Level Structure Segmentations
smsinks/finemapping
A Nextflow framework for finemap
smsinks/ForexConnectAPI
Designed to trade, retrieve live/history price. Intended to be used to build auto-trading robots, custom trading on FXCM accounts.
smsinks/genmap
GenMap - Fast and Exact Computation of Genome Mappability
smsinks/hello-world-MCR
Test code for generating containers using Singularity and Matlab compiler.
smsinks/lean-cli
CLI for running the LEAN engine locally and in the cloud
smsinks/lectures-labs
Slides and Jupyter notebooks for the Deep Learning lectures at Master Year 2 Data Science from Institut Polytechnique de Paris
smsinks/mtdna-mutations
scripts to generate figures/tables from Gorelick et al. Nat Metab, 2021
smsinks/MultiABEL
Multi-Trait Genome-Wide Association Analysis
smsinks/open-data-registry
A registry of publicly available datasets on AWS
smsinks/public-resources
Repository for resources we'd like to share with the community.
smsinks/QUILT
smsinks/SigProfilerExtractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
smsinks/UK_Biobank_GWAS
Overview of the data QC, code, and GWAS summary output from the 2017 UK Biobank data release
smsinks/UKB_pulmonary_function_scripts
smsinks/ukbb_pan_ancestry
Analyses conducting GWAS across the UKBB diverse superpopulations
smsinks/Visual-Style-Prompting
Official Pytorch implementation of "Visual Style Prompting with Swapping Self-Attention"
smsinks/visual_prompting
Exploring Visual Prompts for Adapting Large-Scale Models