naglemi
Postdoctoral researcher at Oregon State University's Forest Biotechnology Lab; PhD in Molecular and Cellular Biology with Biological Data Sciences minor
Oregon State UniversityCorvallis, OR
Pinned Repositories
AgroCulture
AgroCulture
CpGWAS
Tools to support Methylome-wide Association Studies (MWAS), not to be confused with Metabolome-Wide Association Studies (the other MWAS)
cubeglm
Python implementation of general linear model for quantifying fluorophores in fluorescent hyperspectral images
cubeml
Interface to apply machine learning to segmentation of hyperspectral images (hypercubes)
GMOdetectoR
GMOnotebook
Templates for workflows cross-analyzing fluorescent hyperspectral regression with deep segmentation to study plant tissue culture transformation rates
gpt-revcomp-eval
Evals for GPT model abilities to provide reverse complements of DNA sequences
InPlantaGWAS
mtmcskat
Cluster-friendly interface for SKAT with adaptive resampling, multi-threading over SNP windows and permutations, and higher-level parallelization over chromosomes/scaffolds.
terminal_jupyter_intro
Introduction tutorial for command line basics
naglemi's Repositories
naglemi/cubeglm
Python implementation of general linear model for quantifying fluorophores in fluorescent hyperspectral images
naglemi/mtmcskat
Cluster-friendly interface for SKAT with adaptive resampling, multi-threading over SNP windows and permutations, and higher-level parallelization over chromosomes/scaffolds.
naglemi/GMOdetectoR
naglemi/InPlantaGWAS
naglemi/GMOnotebook
Templates for workflows cross-analyzing fluorescent hyperspectral regression with deep segmentation to study plant tissue culture transformation rates
naglemi/gpt-revcomp-eval
Evals for GPT model abilities to provide reverse complements of DNA sequences
naglemi/AgroCulture
AgroCulture
naglemi/CpGWAS
Tools to support Methylome-wide Association Studies (MWAS), not to be confused with Metabolome-Wide Association Studies (the other MWAS)
naglemi/cubeml
Interface to apply machine learning to segmentation of hyperspectral images (hypercubes)
naglemi/dpl_u19
Deep Learning for Life Scientists Pilot
naglemi/GMOlabeler
Python/R code for cross-analyzing fluorescence and semantic segmentation results to calculate statistics for development of specific transgenic plant tissues
naglemi/Pheno_odk_test
A test repo demonstrating design pattern -based phenotype ontology development using the Ontology Development Kit
naglemi/terminal_jupyter_intro
Introduction tutorial for command line basics
naglemi/DenseNet
Contamination Classification DenseNet
naglemi/elastictorch
Pytorch implementation of ElasticNet, intended for investigative benchmarking at this time.
naglemi/evals
Evals is a framework for evaluating LLMs and LLM systems, and an open-source registry of benchmarks.
naglemi/factorimg
Simple Python package to evaluate color palettes in semantic segmentation masks
naglemi/GMOGUI
Graphical interface for the high-throughput phenotyping of plant transformation and regeneration (GMOdetector)
naglemi/rslurm
Submit R code to a Slurm cluster
naglemi/T-LOC
naglemi/TensorFlow-Examples
TensorFlow Tutorial and Examples for Beginners with Latest APIs