Devin-jun

ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.

DUSTED

Dual-attention Enhanced Spatial Transcriptomics Denoiser

esm

tfold

open source code for Tencent tFold

CD-GPT

A Biological Foundation Model Bridging the Gap between Molecular Sequences Through Central Dogma

bart-it

Pre-training BART model for the Italian Language

cell2sentence-ft

Cell2Sentence turns scRNA-seq data into text for LLM training.

PEFF

Repository for the PSI Extended FASTA Format

llm-action

本项目旨在分享大模型相关技术原理以及实战经验。

LLMsNineStoryDemonTower

【LLMs九层妖塔】分享 LLMs在自然语言处理（ChatGLM、Chinese-LLaMA-Alpaca、小羊驼 Vicuna、LLaMA、GPT4ALL等）、信息检索（langchain）、语言合成、语言识别、多模态等领域（Stable Diffusion、MiniGPT-4、VisualGLM-6B、Ziya-Visual等）等 实战与经验。

ProForma

HUPO-PSI Standardized peptidoform notation

ProteoformNomenclatureStandard

ProForma, a Proteoform Notation Standard

ProteinWorkshop

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

SHA-SpatialHeterogeneityAnalysis

A toolkit for genomics spatial heterogeneity analysis

single-cell-transformer-papers

deep_learning_in_proteomics

A list of tools on proteomics using deep learning

cytopus

Single cell omics biology annotations

alphabase

Infrastructure of AlphaX ecosystem

alphapeptdeep

Deep learning framework for proteomics

esm

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

Awesome-Graph-LLM

A collection of AWESOME things about Graph-Related LLMs.

acad-homepage.github.io

AcadHomepage: A Modern and Responsive Academic Personal Homepage

pySankey

create sankey diagrams with matplotlib

scib-pipeline

Snakemake pipeline that works with the scIB package to benchmark data integration methods.

Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

TOSICA

Transformer for One-Stop Interpretable Cell-type Annotation

awesome-deep-learning-single-cell-papers

tuning_playbook

A playbook for systematically maximizing the performance of deep learning models.

GraphGym

Platform for designing and evaluating Graph Neural Networks (GNN)

SDCN

Structural Deep Clustering Network