Pinned Repositories
creme-nn
https://www.biorxiv.org/content/10.1101/2023.07.03.547592v1
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
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)
GOPHER
Toolset for training quantitative sequence to function models.
learning_sequence_motifs
"Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks" by Peter K. Koo and Sean R. Eddy
residualbind
"Global Importance Analysis: A Method to Quantify Importance of Genomic Features in Deep Neural Networks" by Koo et al.
squid-nn
surrogate quantitative interpretability for deepnets
tensorflow_tutorial_genomics
A collection of TensorFlow tutorials to analyze genomics datasets
tfomics
p-koo's Repositories
p-koo/deepomics
deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis
p-koo/evoaug
Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics
p-koo/residualbind
"Global Importance Analysis: A Method to Quantify Importance of Genomic Features in Deep Neural Networks" by Koo et al.
p-koo/creme-nn
https://www.biorxiv.org/content/10.1101/2023.07.03.547592v1
p-koo/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)
p-koo/GradientCorrection
p-koo/tfomics
p-koo/evoaug-tf
Evolution-inspired data augmentations for TensorFlow-based models for regulatory genomics
p-koo/evoaug_analysis
p-koo/GOPHER
Toolset for training quantitative sequence to function models.
p-koo/wrangler_old
data wrangling for genomics data
p-koo/evoaug-tf_analysis
p-koo/gradient_correction
p-koo/squid-nn
surrogate quantitative interpretability for deepnets
p-koo/wrangler
p-koo/libre
p-koo/chromo
p-koo/ConvolutionalAttention
p-koo/CREME_paper_reproducibility
p-koo/degu
p-koo/DREAM-2022-Submission-High_Schoolers_Are_All_You_Need
High Schoolers Are All You Need Team
p-koo/hominid
p-koo/hybrid_genomics
p-koo/model_zoo
p-koo/p-koo.github.io
p-koo/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)
p-koo/robustness
p-koo/squid-nn-old
surrogate quantitative interpretability for deepnets
p-koo/test_gpu
p-koo/tfmodisco-lite
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.