p-koo

deepomics

deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis

evoaug

Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics

residualbind

"Global Importance Analysis: A Method to Quantify Importance of Genomic Features in Deep Neural Networks" by Koo et al.

creme-nn

https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2

exponential_activations

"Improving representations of genomic sequence motifs in convolutional networks with exponential activations" by Koo and Ploenzke (https://doi.org/10.1101/2020.06.14.150706)

GradientCorrection

tfomics

evoaug-tf

Evolution-inspired data augmentations for TensorFlow-based models for regulatory genomics

evoaug_analysis

GOPHER

Toolset for training quantitative sequence to function models.

wrangler_old

data wrangling for genomics data

evoaug-tf_analysis

gradient_correction

squid-nn

surrogate quantitative interpretability for deepnets

wrangler

libre

chromo

ConvolutionalAttention

CREME_paper_reproducibility

degu

DREAM-2022-Submission-High_Schoolers_Are_All_You_Need

High Schoolers Are All You Need Team

hominid

hybrid_genomics

model_zoo

p-koo.github.io

pEMv2

sytems-level diffusion analysis for single particle tracks undergoing normal/non-normal diffusion that can transition between diffusion states (https://journals.aps.org/pre/abstract/10.1103/PhysRevE.94.052412)

robustness

squid-nn-old

surrogate quantitative interpretability for deepnets

test_gpu

tfmodisco-lite

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.