Zhang Lab

deep_learning_in_proteomics

A list of tools on proteomics using deep learning

WebGestaltR

R package for WebGestalt

AutoRT

AutoRT: Peptide retention time prediction using deep learning

OmicsEV

A tool for large scale omics datasets evaluation

neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

COSMO

COSMO: COrrection of Sample Mislabeling by Omics

PepQuery

PepQuery: a targeted peptide search engine

sumer

SUmmarizing Multiple Enrichment analysis Results

proms

protein markers selection

DeepRescore

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

clinicalomicsdbR

R package for interfacing with ClinicalOmicsDB

NetSAM

Network Seriation And Modularization R package

SEPepQuant

SEPepQuant: a graph theory-based approach enables comprehensive protein isoform characterization in shotgun proteomics

DeepRescore2

DeepRescore2: deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification

funmap

generate gene co-function networks using omics data

DeepVEP

webgestalt_rust

Rust implementation of WebGestalt

webgestaltpy

Python package for WebGestalt

bzhanglab.github.io

Zhang Lab

CoPheeMap

Co-regulation map of phosphosites

funmap_aml

funmap_visualization

GENCODE_V42_reference

Reference preparation for proteogenomics data processing and downstream analysis

LinkedOmicsKB_manuscript

Core scripts for calculating associations

neoflow2

neoflow_html_reporter

nf-docker

docker files for pipeline steps

nf-rnaseq

rnaseq pipeline with nextflow

py-pgatk

Python tools for proteogenomics analysis toolkit

TAAPrediction