drisso

sgdGMF

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

SpatialData

spartaco

This package implements the model proposed by A. Sottosanti and D. Risso in 'Co-clustering of Spatially Resolved Transcriptomic Data'.

CPSC393ParlettPelleriti

Algorithm_Fairness_Teachable_Unit

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.

large-scale-data-base

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

FAVITES

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Hackathon

Multi-omics studies are available here

matchSCore2

CSAMA

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

scRNAseq

Clone of the Bioconductor repository for the scRNAseq package.

OrchestratingSingleCellAnalysis-release

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

TENxBrainData

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

projectR

scrattch.hicat

Hierarchical, iterative clustering for analysis of transcriptomics data in R

sc_mixology

This contains the dataset for comparing scRNA-seq analysis methods

c-cpp-notes

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

tabula-muris-vignettes

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

scmap

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

MOFA

Multi-Omics Factor Analysis

clustree

Visualise Clusterings at Different Resolutions

zinbwaveZinger

Integrating zingeR with ZINB-WaVE weights

DECENT

Differential Expression with Capture Efficiency adjustmeNT

simulator

An Engine for Running Simulations

MatrixEval2017

Evaluating access and memory usage of different matrix types

SCnorm

Normalization for single cell RNA-seq data

restfulSE

demonstration of SummarizedExperiment with assay component retrieved from remote HDF5 server

2017-05-us-health-care

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-health-care

WhatData

Datasets Available in R

TENxGenomics

Interface to 10x Genomics' 1.3 m single cell data set