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autort

AutoRT: Peptide retention time prediction using deep learning

benchmark_phospho_identification

Deep learning-derived evaluation metrics enable effective benchmarking of computational tools for phosphopeptide identification

bzhanglab.github.io

Zhang Lab

canprovar

Human Cancer Proteome Variation Database

clinicalomicsdbr

R package for interfacing with ClinicalOmicsDB

copheemap

Co-regulation map of phosphosites

cosmo

COSMO: COrrection of Sample Mislabeling by Omics

customprodbj

data_format

deep_learning_in_proteomics

A list of tools on proteomics using deep learning

deeplfq

protein iBAQ calculation module

deeprescore

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

deeprescore2

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

deepvep

extract_epic_probe

extract TSS upstream and CpG island probes from the EPIC methylation manifest file

funmap

generate gene co-function networks using omics data

funmap_aml

funmap_visualization

gencode_v42_reference

Reference preparation for proteogenomics data processing and downstream analysis

genomicwidgets

gistic2_example

a example script and reference files to run GISTIC2

glad4u

Gene List Automatically Derived For You (GLAD4U)

linkedomicskb_manuscript

Core scripts for calculating associations

lokki

An automatic machine learning framework for 16s metagenomic data

neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

neoflow2

neoflow_html_reporter

neoflow_input_from_pdc

Scripts to prepare input table for NeoFlow 2.0 from PDC and GDC

netgestalt-pub

A data integration framework that allows simultaneous presentation of large-scale experimental and annotation data from various sources in the context of a biological network to facilitate data visualization, analysis, interpretation, and hypothesis generation.

netsam

Network Seriation And Modularization R package