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alphafold

Open source code for AlphaFold.

bcbio

scripts for bcbio RNASeq analysis pipeline

cell_cycle_reporter

conversion_tools

A repository for demo collections

deepgrn

Deep learning for modeling gene regulatory network

enqa

A 3D-equivariant neural network for protein structure accuracy estimation

factornet

A deep learning package for predicting TF binding

finalproject-xinhero-

gene4x

Community detection on gene multiplex

gitignore

A collection of useful .gitignore templates

gnet2

Gene regulatory network modeling tool (GNET2)

gnet2_benchmark

Data and code for benchmark of GNET2

interactivenetworks

Web tool for interactive gene network analysis and visualization.

interpretcontactmap

Deep learning methods for interpreting protein contact maps

keras_svcca

markdown_readme

Markdown - you can mark up titles, lists, tables, etc., in a much cleaner, readable and accurate way if you do it with HTML.

msda

neu-cs5800

Code for CS5800 that I teach at Northeastern University.

numpy_and_mnist_with_convolution_networks

This is a simple demo for convolution neural networks with Numpy only on Python. The sample inputs are from MINST.

phospho_network

Regression Model Based on Prior Network Knowledge

pl_test

pl_test

ratio-distribution-analysis-demo

Software implementation for The Gene Balance Hypothesis: Dosage effects in plant

rnaseq

se3-transformer-public

code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503

simple-implementation-of-ml-algorithms

My simplest implementations of common ML algorithms

viper_copy

viper_infer

Example scripts for VIPER inferences