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/AncesTree
An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data
smsinks/bmapathway
MATLAB source code to accompany the PLoS Genetics paper, "Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease".
smsinks/Calling-Python-from-Matlab
smsinks/Circleplot
Class Circleplot Project
smsinks/dreamtools
Code sharing related to DREAM challenges
smsinks/Easy-T-test-and-Plots
Perform T-test, Automated Transformation, Plotting and Reporting
smsinks/magnum-app
Java app for GWAS pathway and network analysis. This is the repository for the app, there is a separate repository for the command-line tool.
smsinks/matlab-docker
Docker Image with Matlab Compiler Runtime and SSHD
smsinks/MatlabOanda_Wrapper
Matlab wrapper for oanda API
smsinks/multi-dendrix
smsinks/mutex
Automatically exported from code.google.com/p/mutex
smsinks/octave-networks-toolbox
A set of graph/networks analysis functions in Octave
smsinks/Paradigm
PAthway Representation and Analysis by Direct Inference on Graphical Models
smsinks/paradigm-scripts
smsinks/paradigmshift
smsinks/Reference-Interval-Matlab
smsinks/SIDER2
Calculating compound similarities using side effects and indications extracted from drug labels
smsinks/stuartlab-circleplotter-py
python tool for drawing CircleMap images
smsinks/TCGA_differential_expression
Differential expression analysis on TCGA samples.
smsinks/TCGA_RNASeq_Clinical