Statistical software and methods
Code for implementing test to identify differential correlation
R Shiny app to assist with bisulfite sequencing study design
MACAU software for binomial mixed effects modeling
- Described in: AJ Lea*, M Subramaniam*, A Ko, T Lehtimäki, E Raitoharju, M Kähönen, I Seppälä, N Mononen, OT Raitakari, M Ala-Korpela, P Pajukanta, NA Zaitlen*, JF Ayroles*. 2019. Genetic and environmental perturbations lead to regulatory decoherence. eLife, 8:e40538 [link].
- Code available here.
R Shiny app to assist with bisulfite sequencing study design
- Described in: AJ Lea, PAP Durst, TP Vilgalys, J Tung. 2017. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. Nature Ecology and Evolution, 1:1074-1083 [link].
- R Shiny app available here.
MACAU software for binomial mixed effects modeling
Laboratory protocols
mSTARR-seq protocol and vector
- Described in: AJ Lea, CM Vockley, RA Johnston, CA Del Carpio, LB Barreiro, TE Reddy, J Tung. 2018. Genome-wide quantification of the effects of DNA methylation on human gene regulation. eLife, 7:e37513 [link].
- Complete protocol available here.
- pmSTARRseq vector available from Addgene. See details here.
Data use agreements
| oahelp_dua_8may24.docx |
| thgp_dua_1may24.docx |