proteogenomics

There are 1 repository under proteogenomics topic.

• wenbostar / PDV

  PDV: an integrative proteomics data viewer

  proteomicsproteogenomicsmsmsvisulizationbioinformaticsspectra-visualizationpsm
  Language:Java 41

• nf-core / quantms

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

  nf-corenextflowworkflowpipelineproteomicsmass-spectrometryproteogenomicstmtlfqmass-specdiaopenms
  Language:Nextflow 26

• smith-chem-wisc / mzLib

  Library for mass spectrometry projects

  mass-spectrometrychemical-formulasisotopeschemistryspectra-filesproteogenomicsproteomics-datamass-spectrometry-data
  Language:C# 25
• quantms

  bigbio / quantms

  Quantitative mass spectrometry workflow.

  proteomicsproteogenomicstmtlfqmass-spectrometry
  Language:Nextflow 20

• bzhanglab / neoflow

  NeoFlow: a proteogenomics pipeline for neoantigen discovery

  novel-peptide-identificationsneoantigen-predictionneoantigen-discoveryproteogenomicsnextflow-pipeline
  Language:Nextflow 19

• bigbio / py-pgatk

  Python tools for proteogenomics analysis toolkit

  pythonproteogenomicsensemblproteomicsmass-spectrometryvcfproteogenomics-analysis-toolkit
  Language:Python 9

• bzhanglab / PepQuery

  PepQuery: a targeted peptide search engine

  mass-spectrometryproteogenomicsproteomicspeptide-identification
  Language:Java 7

• wenbostar / Customprodbj

  Customized protein database construction

  proteogenomicsproteomicsbioinformatics
  Language:Java 7

• bigbio / pgatk

  PGATK: ProteoGenomics Analysis ToolKit

  proteogenomicsproteomicsgenomicsbioinformatics
  6

• EuBIC / ReproducibleMSGuidelines

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

  mass-spectrometryproteogenomicsproteomicsmetabolomicslipidomicsguidelinesopenaccess
  Language:JavaScript 6

• smith-chem-wisc / Spritz

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

  bioinformaticsproteogenomicssnakemakesnakemake-pipelinerna-seqproteomics
  Language:C# 6

• wenbostar / PGA

  PGA: a tool for ProteoGenomics Analysis

  proteogenomicsproteomicsgenomicstranscriptomics
  Language:R 6

• linas / biome-distribution

  Research into statistical distributions of genomes, proteomes and reactomes

  genomic-data-analysisgenomics-visualizationproteomicsproteogenomicsreactomereactome-pathway
  Language:Scheme 5

• nf-core / pgdb

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

  nf-corenextflowworkflowpipelineproteogenomicsproteomicspypgatkprotein-databasescosmicgnomad
  Language:Nextflow 5

• ProGenNo / ProHap

  Proteogenomics database-generation tool for protein haplotypes and variants

  haplotypesproteogenomicsprotein-database-generation
  Language:Python 5

• uclahs-cds / package-moPepGen

  Multi-Omics Peptide Generator

  cancer-genomicsneoantigenproteogenomicsproteomicsgenomics
  Language:Python 5

• brianrisk / Peppy

  6-frame proteogenomic peptide-spectrum match identification engine

  proteogenomicsproteomics
  Language:Java 3

• bigbio / pgdb

  ProteomeGenomics Database Creation - Nextflow Pipeline

  proteogenomicsnf-corenextflowmass-spectrometryproteomicsensemblcosmic
  Language:Nextflow 2

• abiswas97 / DeNoPro

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

  novel-peptide-identificationsproteogenomics
  Language:Python 1

• anuragraj / ProteoLib

  Library for Proteomics research literatures, tools and databases.

  proteomicsproteogenomics
  Language:HTML 1

• AstraBert / saccharomyces-pythia

  Saccharomyces cerevisiae information, gene calling and ORF identification assistant

  aichatbot-applicationgene-callinggenerative-aigenomicsgradiomachine-learningmodel-organismspilot-projectproteogenomicsresearch-assistantsaccharomyces-cerevisiaesequence-classification
  Language:Python 1

• bigbio / pgatk-io

  High performance io library for proteogenomics

  sparkproteomicsfileformatsparquetmass-spectrometryproteogenomics
  Language:Java 1

• bigbio / pgt-pangenome

  Protegenomics analysis based on Pangenome references

  mass-spectrometrynon-canonicalpangenomeproteinproteogenomicsproteomicsvariantspublic-proteomicsquantms
  Language:Jupyter Notebook 1

• chinmayaNK22 / Proteogenomic-Pipeline

  Python packages for easy execution of proteogenomic workflow

  proteogenomics-analysis-toolkitproteogenomicsproteomicsgssps
  Language:Python 1

• YueAndyQi / lncRNA_immunopeptidome_Scripts

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

  epitope-discoverycancerproteomicsnon-canonicalproteogenomics
  Language:Python 1

• anuragraj / PgxSAVy

  A tool for quality control and annotation of variant peptides after FDR in proteogenomics

  proteogenomicsproteomicsvariantsmass-spectrometryscoring
  Language:Perl 0

• beherasan / ProteoGenomics

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

  proteogenomics
  Language:Perl 0

• CPL-SeongminCheon / Trypsin_LysC_InSilico_Digestion

  In Silico Trypsin/Lys-C Clevage Site Prediction

  proteomicsproteomics-data-analysisbioinformatics-toolproteogenomics
  Language:Python 0

• npinter / ProteoGenDB

  ProteoGenDB: A Fast Proteogenomic Pipeline for Identifying Sequence Variants in Proteomics Data

  bioinformaticsmass-spectrometryproteogenomicsproteomics
  Language:Python 0

• bigbio / quantms-utils

  A python library with scripts and helpers classes for quantms workflow

  bigdatacloudmass-spectrometrynextflowproteogenomicsproteomics
  Language:Python

• srithegreat / codephoenix

  My codes for proteomics, genomics and proteogenomics

  proteomicsproteogenomicsgenomicspythongenomic-data-analysis
  Language:Python