vdemichev

timsrust

Scalable-DIA-NN

Scalable workflow to run https://github.com/vdemichev/DiaNN on NCI Gadi HPC

oktoberfest

Rescoring and spectral library generation pipeline for proteomics.

AutoGPT

AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

RWKV-LM

RWKV is an RNN with transformer-level LLM performance. It can be directly trained like a GPT (parallelizable). So it's combining the best of RNN and transformer - great performance, fast inference, saves VRAM, fast training, "infinite" ctx_len, and free sentence embedding.

rwkv.cpp

INT4/INT5/INT8 and FP16 inference on CPU for RWKV language model

llama.cpp

LLM inference in C/C++

PDD-shiny

Processing of DIA-NN Data

synthedia

Create synthetic DIA LC-MS/MS for proteomics experiments

advent-of-code-2022-with-chat-gpt

Solving Advent of Code 2022 with ChatGPT

stable-diffusion

A latent text-to-image diffusion model

sage

Proteomics search & quantification so fast that it feels like magic

DIAgui

An interactive shiny app for processing DIA-nn output (filtering, MaxLFQ, Top3, iBAQ, etc.)

Protein-Contaminant-Libraries-for-DDA-and-DIA-Proteomics

This project is created by the Hao Lab at the Chemistry Department in George Washington University, Washington, D.C. This project aims to provide contaminant protein FASTA and spectral libraries that can be universally applied to DDA and DIA proteomics and freely accessible for the proteomics community.

casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

alphamap

An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.

msdap

MS-DAP: downstream analysis pipeline for quantitative proteomics

esquisse

RStudio add-in to make plots interactively with ggplot2

DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.

MiniDNN

A header-only C++ library for deep neural networks

pDeep3

MS/MS prediction for peptides

proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

torchnca

A PyTorch implementation of Neighbourhood Components Analysis.

pyphe

Python toolbox for phenotype analysis of arrayed microbial colonies

DeepDIA

Using deep learning to generate in silico spectral libraries for data-independent acquisition analysis.

FragPipe

A cross-platform proteomics data analysis suite

auto-py-to-exe

Converts .py to .exe using a simple graphical interface

Proteomics_linear_modeling

Short workshop to demonstrate some uses of linear modeling in proteomics

prosit

Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7