GitHub topics: proteogenomics
smith-chem-wisc/mzLib
Library for mass spectrometry projects
Language: C# - Size: 289 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 26 - Forks: 37
Nesvilab/PepCentric
Search proteins and peptides against repository-scale MS/MS spectra within seconds
Size: 6.84 KB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0
sheltzer-lab/DosageCompensationFactors
This project contains the code for the manuscript "Explainable Machine Learning Identifies Factors for Dosage Compensation in Aneuploid Human Cancer Cells" by Heller et al. (https://doi.org/10.1101/2025.05.12.653427).
Language: R - Size: 1.27 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0
bigbio/quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Language: Nextflow - Size: 25 MB - Last synced at: about 19 hours ago - Pushed at: 13 days ago - Stars: 56 - Forks: 45
npinter/ProteoGenDB
ProteoGenDB: A Fast Proteogenomic Pipeline for Identifying Sequence Variants in Proteomics Data
Language: Python - Size: 639 KB - Last synced at: 1 day ago - Pushed at: 26 days ago - Stars: 1 - Forks: 0
uclahs-cds/package-moPepGen
Multi-Omics Peptide Generator
Language: Python - Size: 9.48 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 23 - Forks: 4
Xinglab/ProteoSeq
ProteoSeq: Protein Isoform Analysis via Long-read RNA-seq
Language: Python - Size: 71.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
bzhanglab/PepQueryMHC
PepQueryMHC: Rapid and Comprehensive Tumor Antigen Prioritization from Immunopeptidomics Data
Language: Java - Size: 238 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0
ProGenNo/ProHap
Proteogenomics database-generation tool for protein haplotypes and variants
Language: Python - Size: 8.82 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 11 - Forks: 3
bigbio/quantms-utils
A python library with scripts and helpers classes for quantms workflow
Language: Python - Size: 80.6 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1
wenbostar/PDV
PDV: an integrative proteomics data viewer
Language: Java - Size: 5.97 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 46 - Forks: 20
bigbio/py-pgatk
Python tools for proteogenomics analysis toolkit
Language: Python - Size: 125 MB - Last synced at: 21 days ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 12
bigbio/pgdb
ProteomeGenomics Database Creation - Nextflow Pipeline
Language: Nextflow - Size: 2.9 MB - Last synced at: 1 day ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 11
nf-core/pgdb Fork of bigbio/pgdb
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
Language: Nextflow - Size: 3.07 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 5 - Forks: 8
linas/biome-distribution
Research into statistical distributions of genomes, proteomes and reactomes
Language: Scheme - Size: 14.2 MB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 0
bzhanglab/neoflow
NeoFlow: a proteogenomics pipeline for neoantigen discovery
Language: Nextflow - Size: 4.01 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 22 - Forks: 12
AstraBert/saccharomyces-pythia
Saccharomyces cerevisiae information, gene calling and ORF identification assistant
Language: Python - Size: 9.9 MB - Last synced at: 7 days ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0
smith-chem-wisc/Spritz
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
Language: C# - Size: 34.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 11
bigbio/pgt-pangenome
Protegenomics analysis based on Pangenome references
Language: Jupyter Notebook - Size: 595 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
nf-core/quantms 📦
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Language: Nextflow - Size: 21.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 26 - Forks: 28
anuragraj/PgxSAVy
A tool for quality control and annotation of variant peptides after FDR in proteogenomics
Language: Perl - Size: 1.98 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
chinmayaNK22/Proteogenomic-Pipeline
Python packages for easy execution of proteogenomic workflow
Language: Python - Size: 24.4 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1
EuBIC/ReproducibleMSGuidelines
This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.
Language: JavaScript - Size: 332 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 1
bzhanglab/PepQuery
PepQuery: a targeted peptide search engine
Language: Java - Size: 321 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0
bigbio/pgatk-io
High performance io library for proteogenomics
Language: Java - Size: 72.4 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0
wenbostar/PGA
PGA: a tool for ProteoGenomics Analysis
Language: R - Size: 187 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 10
wenbostar/Customprodbj
Customized protein database construction
Language: Java - Size: 38.1 KB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 4
brianrisk/Peppy
6-frame proteogenomic peptide-spectrum match identification engine
Language: Java - Size: 33.2 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0
bigbio/pgatk
PGATK: ProteoGenomics Analysis ToolKit
Size: 130 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 5
abiswas97/DeNoPro
Denovo Proteogeomics pipeline to identify clinically relevent novel variants from RNAseq and Proteomics data.
Language: Python - Size: 202 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0
anuragraj/ProteoLib
Library for Proteomics research literatures, tools and databases.
Language: HTML - Size: 6.6 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1
beherasan/ProteoGenomics
Proteomic evidences can improve the existing genome annotation by finding novel coding regions or genome reannotations. These scripts can perform such tasks.
Language: Perl - Size: 6.84 KB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
srithegreat/codephoenix
My codes for proteomics, genomics and proteogenomics
Language: Python - Size: 50.8 KB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
