Tarmo Äijö's repositories
GPMicrobiome
A novel probabilistic approach to explicitly model overdispersion and sampling zeros in 16S rRNA sequencing data by considering the temporal correlation between nearby time points using Gaussian Processes
Lux
Lux is an integrative hierarchical Bayesian model for analyzing any combination of BS-seq/oxBS-seq/TAB-seq/fCAB-seq/CAB-seq/redBS-seq/MAB-seq/etc data enabling accurate and unbiased quantification of different cytosine modifications (C/5mC/5hmC/5fC/5cac) and differential methylation at individual cytosines or loci, with or without replicates, while taking imperfect experimental parameters into account.
LuxGLM
LuxGLM is a method for quantifying oxi-mC species with arbitrary covariate structures from bisulphite based sequencing data. LuxGLM's probabilistic modeling framework combines a previously proposed hierarchical generative model of Lux for oxi-mC-seq data and a general linear model component to account for confounding effects.
trainerroad-to-text
Conversion of TrainerRoad workouts to text
numpyro
Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.
outlines
Structured Text Generation
raesymatto
Raesymatto: visualize genomic data