mzc2113391

scANNA

The main repository hosting the implementation of scANNA (single-cell ANalysis using Neural Attention)

cPeaks

Consensus peaks of chromatin accessibility in the human genome

simba

SIMBA: SIngle-cell eMBedding Along with features

scGPT

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

giggle

Interval data structure

tf-bind-transformer

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

pyBigWig

A python extension for quick access to bigWig and bigBed files

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

GLUE

Graph-linked unified embedding for single-cell multi-omics data integration

awesome-deep-learning-single-cell-papers

Intro-to-ChIPseq

Intro to ChIPseq using HPC

Statistical-Learning-Method_Code

手写实现李航《统计学习方法》书中全部算法

pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks

Machine-learning-for-proteins

Listing of papers about machine learning for proteins.

ColabDesign

Making Protein Design accessible to all via Google Colab!

pubmed_parser

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

PubMed2PDF

A Python package to download full article PDFs from OA publications

HiCLift

A fast and efficient tool for converting chromatin interaction data between genome assemblies

Pore-C-Snakemake

Lhy_Machine_Learning

李宏毅2021/2022/2023春季机器学习课程课件及作业

RFdiffusion

Code for running RFdiffusion

OpenComplex

Trainable PyTorch framework for developing protein, RNA and complex models.

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