Aedin Culhane's repositories
PCAworkshop
An introduction to matrix factorization and PCA and SVD.
eHealthHub
Website for the all-island eHealth-Hub For Cancer
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Aedin.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
beacon2-ri-api
Beacon v2 Reference Implementation (API)
BestPracticesST
'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book
bioc-project
Introduction to the Bioconductor project
BioC2022
BioC2022 conference material
bioconductor.org
Website for bioconductor.org
BiocReporting
Public repo for Bioconductor project reporting 2022
biocypher
A unifying framework for biomedical research knowledge graphs
CommonDataModel
Definition and DDLs for the OMOP Common Data Model (CDM)
conference
A jekyll-built conference website template
dynbenchmark
Comparison of methods for trajectory inference on single-cell data 🥇
EunomiaDatasets
Hosting of sample CDM datasets in CSV format for use in testing in Darwin.
geneSetVis
gene-set enrichment visualization.
htsget-refserver
Reference server implementation for the GA4GH HTSget API standard.
metadata-schema
This repo is for the metadata schemas associated with the HCA
OHCA4AnVIL
AnVIL Docker Image for OCHA book
omop-etl
ETL Tool for converting datasets to OMOP CDM
OncologyWG
Oncology Working Group Repository
PLM-ICD
PLM-ICD: Automatic ICD Coding with Pretrained Language Models
scRNAseqBasicWorkflow
A short workflow with a basic scRNAseq workflow extracted and extended from the Unfiltered human PBMCs (10X Genomics) workflows in the "Orchestrating Single Cell Analysis with Bioconductor" book. This was cloned from https://github.com/OSCA-source/OSCA.workflows, edited and extended. Dep
SNPcheck
R package for using SNPs to QC HTO and LMO demultiplexing calls
TREEHOOSE
DARE UK Sprint Project: Trusted Research Environment and Enclave for Hosting Open Original Science Exploration
VIBE2022.github.io
Jekyll template for a conference website containing program, speaker, talks and room overview