mzc2113391

3DMax

A maximum likelihood method for reconstructing 3D chromosome structure from chromosomal contact data

caesar

An accurate and interpretable computational model for predicting nucleosome resolution chromatin contact maps

Neural-Network-Theory-and-Applications-Homework-SJTU2018

上海交通大学CS系研究生神经网络课程学习材料

Guideline-for-Computational-Biology-and-Bioinformatics

paper-reading

深度学习经典、新论文逐段精读

stable-diffusion

A latent text-to-image diffusion model

HiPore-C

We developed a protocol of in situ high throughput multi-way contact long read Pore-C sequencing (in situ HiPore-C), a strategy that integrated multi-fragment ligates preparation with third-generation sequencing technology. With HiPore-C approach, we could explore higher-order chromatin interaction genome-widely.

so-vits-svc

SoftVC VITS Singing Voice Conversion

dance

DANCE: a deep learning library and benchmark platform for single-cell analysis

ChromFormer

Network_expansion

The following repository contain two functions needed for the network expansion method as descibed in doi: https://doi.org/10.1101/2021.07.19.452924

PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

HiConfidence

This package helps to construct confidence matrices for Hi-C replicates

Friman_etal_ULI

Source code for custom analysis performed for Friman et al. 2023 (Genome Research)

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

Hi-C-LSTM

Hi-C-LSTM is a framework to form Hi-C representations that are useful for tasks such as element identification and in-silico modification.

folding_tools

A collection of *fold* tools

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins