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followers: 44.0 following: 39.0 repos: 81.0 gists: 11.0

Name: Alan O'Callaghan

Type: User

Company: University of Edinburgh

Bio: Biomedical data - stats - programming

Location: Edinburgh

Blog: https://alanocallaghan.github.io

I work on statistics and machine learning in biomedical data. At the moment I am working on the QuPath project, helping to improve and expand QuPath's ability to perform image analysis workflows in a variety of data types. Previously I worked on modelling of eQTLs using allele specific expression in celltype-specific studies of immune-mediated diseases, and before that on quantifying expression heterogeneity in single cell RNAseq data using a Bayesian approach.

I maintain some R packages:

CRAN packages:
- bayefdr
- contrast
Bioc packages:

Package Devel Release Issues Pull requests

snifter

densvis

scater

BASiCStan

I currently maintain two parts of the Bioconductor book ecosystem:

Book/Chapter	Devel	Release	Issues	Pull requests
OSCA	devel	release
OSCA.multisample	devel	release

I also contribute to:

CRAN packages:
- heatmaply
Bioc:

Package Devel Release Issues Pull requests

BASiCS

Some other stuff:

plotlyutils: cool plotting ideas with plotly
shinystats: shiny apps to demonstrate statistical ideas.

Alan O'Callaghan's Projects

qupath-extension-wsinfer

QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/

qupath-fxtras

Reusable JavaFX tools for QuPath (and beyond)

qupath-r-extension

qupath-scripting-setups

qust

QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis

r-pkgs

My R library

r2guess

Wrapper functions for GUESS

scalability_benchmarks

Benchmarks for scalability code

scater

Clone of the Bioconductor repository for the scater package.

scuttle

Clone of the Bioconductor repository for the scuttle package.

seurat

R toolkit for single cell genomics

shell_scripts

My personal shell scripts

shinystats

Shiny apps to demonstrate statistical concepts

simple-linear-regression-public-health

Simple linear regression for public health

singlecellseq

Batch effects and the effective design of single-cell gene expression studies

slurm

Cookiecutter for snakemake slurm profile

snakemake-qsub

Simple snakemake profile for qsub cluster

snakemake-sync-bq-sub

Snakemake cookiecutter profile for bsub/qsub using cluster-sync (specific for UoE eddie)

snifter

R wrapper for the python openTSNE library

temp_conversion

C temperature conversion CL app

wsinfer

🔥🚀 Blazingly fast pipeline for patch-based classification in whole slide images

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