Pinned 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.
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
Span
A simple js tool to annotate Spatial Transcriptomics (ST) data
Splotch
Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data
trainerroad-to-text
Conversion of TrainerRoad workouts to text
zwog
Grammar-based generation of structured cycling workouts
tare's Repositories
tare/Splotch
Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data
tare/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
tare/zwog
Grammar-based generation of structured cycling workouts
tare/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.
tare/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.
tare/trainerroad-to-text
Conversion of TrainerRoad workouts to text
tare/numpyro
Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.
tare/outlines
Structured Text Generation
tare/raesymatto
Raesymatto: visualize genomic data
tare/Span
A simple js tool to annotate Spatial Transcriptomics (ST) data
tare/Spav
A tool for visualizing Splotch results