hiranumn/ATAC_peak

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Created over 7 years ago
Updated over 7 years ago

hiranumn/ATAC_peak

hiranumn

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Deep learning framework to predict TF binding from DNA-sequence and ATAC-seq signals.

IntegratedGradients

Python/Keras implementation of integrated gradients presented in "Axiomatic Attribution for Deep Networks" for explaining any model defined in Keras framework.

Jupyter Notebook

DeepAccNet

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

DeepATACseq

Repository for the code for DeepATAC project presented at WCB workshop in ICML2017

Jupyter Notebook

IntegratedGradientsTF

Tensorflow implementation of integrated gradients presented in "Axiomatic Attribution for Deep Networks". It explains connections between two tensors.

Jupyter Notebook

DLmodels

Personal experiments and implementation examples of deep learning papers.

Jupyter Notebook

DeepAccNet-TF

Python/TF1 implementation of DeepAccNet (https://www.biorxiv.org/content/10.1101/2020.07.17.209643v1)

LocalAccuracyPredictor

Tensorflow/Python implementation of local accuracy predictor for proteins

Jupyter Notebook

BackpropDemonstration

Demonstration of back-propagation for the undergrad ML class that I TAed [Archived]

PyProtein

An easy interface to extract data from pdbs using the rosetta framework

jlVCF

A simple VCF file parser for Julia 3.0

GraphConv

Implementation of graph convolution layers

Jupyter Notebook

BackboneEstimator.py

Estimates backbone quality based on C beta (or C alpha) distance maps.

Jupyter Notebook

ChipSeqUtil.jl

Utility files for analyzing ChIP-Seq data.

AminoAcids2BackboneAngles

Sample deep-learning notebooks for presentation given at BakerLab @ UW

Jupyter Notebook

jlBAM

A simple bam file reader for Julia 5.0