The Wayback Machine - https://web.archive.org/web/20220516040850/https://github.com/topics/proteogenomics

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proteogenomics

Here are 24 public repositories matching this topic...

wenbostar / PDV

PDV: an integrative proteomics data viewer

bioinformatics psm proteomics msms visulization proteogenomics spectra-visualization

Updated Apr 10, 2022
Java

smith-chem-wisc / mzLib

Library for mass spectrometry projects

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

Updated May 4, 2022
C#

bzhanglab / neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

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

Updated May 13, 2022
Nextflow

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 Feb 19, 2022
C#

bigbio / pgatk

PGATK: ProteoGenomics Analysis ToolKit

bioinformatics genomics proteomics proteogenomics

Updated Aug 19, 2021

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 Nov 18, 2019
JavaScript

wenbostar / Customprodbj

Customized protein database construction

bioinformatics proteomics proteogenomics

Updated Sep 3, 2020
Java

quantms

bigbio / quantms

Quantitative mass spectrometry workflow.

proteomics mass-spectrometry proteogenomics tmt lfq

Updated May 15, 2022
Nextflow

wenbostar / PGA

PGA: a tool for ProteoGenomics Analysis

genomics proteomics transcriptomics proteogenomics

Updated Mar 8, 2022
R

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 13, 2022
Nextflow

bzhanglab / PepQuery

PepQuery: a peptide-centric search engine for novel peptide searching

proteomics mass-spectrometry peptide-identification proteogenomics

Updated Nov 24, 2021

anuragraj / ProteoLib

Library for Proteomics research literatures, tools and databases.

proteomics proteogenomics

Updated Jan 13, 2021
HTML

CPL-SeongminCheon / Trypsin_LysC_InSilico_Digestion

In Silico Trypsin/Lys-C Clevage Site Prediction

proteomics proteogenomics bioinformatics-tool proteomics-data-analysis

Updated Apr 8, 2022
Python

bigbio / py-pgatk

Python tools for proteogenomics analysis toolkit

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

Updated May 10, 2022
Python

abiswas97 / DeNoPro

Denovo Proteogeomics pipeline to identify clinically relevent novel variants from RNAseq and Proteomics data.

proteogenomics novel-peptide-identifications

Updated Jul 14, 2021
Python

beherasan / ProteoGenomics

Proteomic evidences can improve the existing genome annotation by finding novel coding regions or genome reannotations. These scripts can perform such tasks.

Updated Oct 16, 2019
Perl

bigbio / pgatk-io

High performance io library for proteogenomics

spark parquet proteomics mass-spectrometry proteogenomics fileformats

Updated May 8, 2021
Java

YueAndyQi / lncRNA_immunopeptidome_Scripts

Scripts for lncRNA Project is a novel mass spectrometry-based peptide sequencing pipeline of the identification of LncRNA-derived immunopeptidome.

cancer proteomics epitope-discovery proteogenomics non-canonical

Updated Jul 2, 2020
Python

bigbio / pgdb

ProteomeGenomics Database Creation - Nextflow Pipeline

nextflow ensembl proteomics mass-spectrometry cosmic proteogenomics nf-core

Updated May 15, 2022
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 proteogenomics tmt nf-core mass-spec lfq

Updated May 11, 2022
Nextflow

chinmayaNK22 / Proteogenomic-Pipeline

Python packages for easy execution of proteogenomic workflow

proteomics proteogenomics proteogenomics-analysis-toolkit gssps

Updated Feb 18, 2022
Python

srithegreat / codephoenix

My codes for proteomics, genomics and proteogenomics

python genomics proteomics genomic-data-analysis proteogenomics

Updated Jul 27, 2018
Python

ypriverol / pgatk-service

The ProteoGenomics pipelines service using Nexflow, Flask

flask proteomics proteogenomics

Updated Nov 2, 2019
Python

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