Keegan Korthauer 🇨🇦
@keegankorthauer.bsky.social
🧬🖥️ Biologist turned statistician developing tools for (epi)genomics
🇨🇦 Assistant Prof
UBC Stats & BC Children's Hospital Research Institute
https://www.korthauerlab.com/
She/her
🇨🇦 Assistant Prof
UBC Stats & BC Children's Hospital Research Institute
https://www.korthauerlab.com/
She/her
decemedip is available on GitHub and we welcome feedback! github.com/nshen7/decem...
GitHub - nshen7/decemedip: An R package for deconvoluting cell types in bulk-tissue/cell-free MeDIP-seq data leveraging a Bayesian hierarchical model. Depends on RStan.
An R package for deconvoluting cell types in bulk-tissue/cell-free MeDIP-seq data leveraging a Bayesian hierarchical model. Depends on RStan. - nshen7/decemedip
github.com
May 15, 2025 at 7:33 PM
decemedip is available on GitHub and we welcome feedback! github.com/nshen7/decem...
We show that decemedip can identify tissue-of-origin in many bulk tumour samples as well as in cell-free DNA from cancer patients, and these latter estimates are correlated with parallel measurements of circulating tumour DNA content.
May 15, 2025 at 7:33 PM
We show that decemedip can identify tissue-of-origin in many bulk tumour samples as well as in cell-free DNA from cancer patients, and these latter estimates are correlated with parallel measurements of circulating tumour DNA content.
In addition to estimating cell type proportions and their uncertainty intervals, decemedip translates cross-platform measurements between MeDIP-seq counts and fractional methylation levels.
May 15, 2025 at 7:28 PM
In addition to estimating cell type proportions and their uncertainty intervals, decemedip translates cross-platform measurements between MeDIP-seq counts and fractional methylation levels.
We present decemedip, a reference-based model to estimate cell type composition of immunoprecipitation-based DNA methylomes (MeDIP-seq). While tools exist for deconvoluting absolute methylation levels (BS-seq), this is the first approach applicable to efficient affinity-enrichment protocols.
May 15, 2025 at 7:26 PM
We present decemedip, a reference-based model to estimate cell type composition of immunoprecipitation-based DNA methylomes (MeDIP-seq). While tools exist for deconvoluting absolute methylation levels (BS-seq), this is the first approach applicable to efficient affinity-enrichment protocols.
I'd be a bit offended by the LLM's claim to have taken my lecture and made it 'coherent' 😝
January 30, 2025 at 9:23 PM
I'd be a bit offended by the LLM's claim to have taken my lecture and made it 'coherent' 😝