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proteogenomics

Here are 32 public repositories matching this topic...

wenbostar / PDV

PDV: an integrative proteomics data viewer

bioinformatics psm proteomics msms visulization proteogenomics spectra-visualization

Updated May 20, 2024
Java

quantms

bigbio / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

proteomics mass-spectrometry proteogenomics tmt lfq

Updated Nov 29, 2024
Nextflow

nf-core / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

workflow pipeline nextflow proteomics dia mass-spectrometry openms proteogenomics tmt nf-core mass-spec lfq

Updated May 6, 2024
Nextflow

smith-chem-wisc / mzLib

Library for mass spectrometry projects

chemistry mass-spectrometry chemical-formulas isotopes proteomics-data spectra-files proteogenomics mass-spectrometry-data

Updated Nov 19, 2024
C#

bzhanglab / neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

proteogenomics nextflow-pipeline neoantigen-prediction novel-peptide-identifications neoantigen-discovery

Updated Nov 16, 2024
Nextflow

bigbio / py-pgatk

Python tools for proteogenomics analysis toolkit

python vcf ensembl proteomics mass-spectrometry proteogenomics proteogenomics-analysis-toolkit

Updated Apr 26, 2024
Python

bzhanglab / PepQuery

PepQuery: a targeted peptide search engine

proteomics mass-spectrometry peptide-identification proteogenomics

Updated May 1, 2024
Java

wenbostar / PGA

PGA: a tool for ProteoGenomics Analysis

genomics proteomics transcriptomics proteogenomics

Updated Mar 8, 2022
R

wenbostar / Customprodbj

Customized protein database construction

bioinformatics proteomics proteogenomics

Updated Sep 3, 2020
Java

smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

bioinformatics rna-seq snakemake proteomics proteogenomics snakemake-pipeline

Updated Jun 19, 2024
C#

EuBIC / ReproducibleMSGuidelines

This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.

proteomics metabolomics mass-spectrometry guidelines lipidomics openaccess proteogenomics

Updated Sep 25, 2024
JavaScript

bigbio / pgatk

PGATK: ProteoGenomics Analysis ToolKit

bioinformatics genomics proteomics proteogenomics

Updated Aug 19, 2021

uclahs-cds / package-moPepGen

Multi-Omics Peptide Generator

genomics cancer-genomics proteomics proteogenomics neoantigen

Updated Oct 25, 2024
Python

ProGenNo / ProHap

Proteogenomics database-generation tool for protein haplotypes and variants

haplotypes proteogenomics protein-database-generation

Updated Nov 1, 2024
Python

bigbio / quantms-utils

A python library with scripts and helpers classes for quantms workflow

cloud nextflow bigdata proteomics mass-spectrometry proteogenomics

Updated Dec 3, 2024
Python

linas / biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes

proteomics reactome genomic-data-analysis genomics-visualization proteogenomics reactome-pathway

Updated Feb 14, 2022
Scheme

nf-core / pgdb

The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.

workflow pipeline nextflow proteomics cosmic proteogenomics nf-core protein-databases gnomad pypgatk

Updated May 9, 2024
Nextflow

brianrisk / Peppy

6-frame proteogenomic peptide-spectrum match identification engine

proteomics proteogenomics

Updated Sep 4, 2022
Java

AstraBert / saccharomyces-pythia

Saccharomyces cerevisiae information, gene calling and ORF identification assistant

machine-learning ai genomics chatbot-application model-organisms gradio sequence-classification proteogenomics research-assistant saccharomyces-cerevisiae pilot-project generative-ai gene-calling

Updated Apr 15, 2024
Python

bigbio / pgdb

ProteomeGenomics Database Creation - Nextflow Pipeline

nextflow ensembl proteomics mass-spectrometry cosmic proteogenomics nf-core

Updated Jun 22, 2022
Nextflow

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