Machine Learning in R

Make Complex Heatmaps

Collection of various algorithms implemented in R.

R Package for Time Series Clustering Along with Optimizations for DTW

Visualise Clusterings at Different Resolutions

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Starter code of Prof. Andrew Ng's machine learning MOOC in R statistical language

Mathematical & Statistical topics to perform statistical analysis and tests; Linear Regression, Probability Theory, Monte Carlo Simulation, Statistical Sampling, Bootstrapping, Dimensionality reduction techniques (PCA, FA, CCA), Imputation techniques, Statistical Tests (Kolmogorov Smirnov), Robust Estimators (FastMCD) and more in Python and R.

Assessing the purity of single cell population

iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. It supports a variety of single-cell technologies, including scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq, and Spatial Transcriptomics (ST).

Single Cell Cluster Evaluation

Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data

Structured Graph Learning via Laplacian Spectral Constraints (NeurIPS 2019)

Enrichment Networks for Pathway Enrichment Analysis

Process and Analyze Mouse-Tracking Data

Workshop (6 hours): Clustering (Hdbscan, LCA, Hopach), dimension reduction (UMAP, GLRM), and anomaly detection (isolation forests).

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Misc Statistics and Machine Learning codes in R

A R framework for pipeline benchmarking, with application to single-cell RNAseq

simpler single cell RNAseq data clustering