Uncertainty quantification for cell type annotation using conformal inference

Efficient stochastic gradient descent algorithms for the estimation of generalized matrix factorization models in R.

A one week teachable unit about creating fair algorithms, covering different definitions of fairness, the mathematics behind trust scores, and a lab implementing both of these ideas.

Base Rmd files for Orchestrating Large-Scale Data Analysis in Bioconducotr

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Multi-omics studies are available here

Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology

Clone of the Bioconductor repository for the scRNAseq package.

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

An ExperimentHub package for the 1.3 million brain cell 10X single-cell RNA-seq data set.

Hierarchical, iterative clustering for analysis of transcriptomics data in R

This contains the dataset for comparing scRNA-seq analysis methods

Lecture notes and example code for teaching C & C++

Examples analyses using the single-cell RNA-seq data from mouse cell atlases

A tool for unsupervised projection of single cell RNA-seq data

Multi-Omics Factor Analysis

Visualise Clusterings at Different Resolutions

Integrating zingeR with ZINB-WaVE weights

Differential Expression with Capture Efficiency adjustmeNT

An Engine for Running Simulations

Evaluating access and memory usage of different matrix types

Normalization for single cell RNA-seq data

demonstration of SummarizedExperiment with assay component retrieved from remote HDF5 server

Data and R code to reproduce the graphics in the May 24, 2017 BuzzFeed News article, "Why Americans Are So Damn Unhealthy, In 4 Shocking Charts." https://www.buzzfeed.com/peteraldhous/american-heal…

Datasets Available in R