Chinmaya Narayana's repositories
Variant-Proteome-DB-Generator
A python command line based script for extraction of annotated variants from VCF file, generating variant proteome database and to check the uniqueness of variant proteins from the database search.
PTM-Site-Validator
Validation of modified amino acid sites in peptide sequences by identifying immonium ions in the raw spectra (.mgf format)
Blib2OpenSwath
A Python script to convert the spectral library in BLIB format (.blib) from either Skyline or BiblioSpec to readable library format (OpenSwath or Spectronaut libraries)
deep_learning_in_proteomics
A list of tools on proteomics using deep learning
DIA-SpecLib_Result_Summarizer
Extract the identified peptides and proteins from spectral library search of DIA proteomic data in Skyline
General_Scripts-Python
Identification, Counting the number of rows and Deleting of files based on suffix, prefix or other search terms in multiple directories
MGF-file-splitter
Extract raw file specific spectra from an unassigned spectra file (.mgf) from Proteome Discoverer and generate new .mgf files specific to raw files
PepAnnotate
Generate annotated Peptide Spectrum Matches (PSMs) from proteomic database search result
Proteogenomic-Pipeline
Python packages for easy execution of proteogenomic workflow
proteogenomics_python
python scripts for proteogenomics analysis
Proteogenomics_workflow
A proteogenomics approach to identify cancer variants and neoantigens
PTM-Summarizer
Summarize post-translationally modified amino acid sites, peptides and proteins for Proteome Discoverer output
Python-Scripts
Scripts used for proteomic data formatting and extraction
SpecLib_Feature_Extractor
Extracts the features of peptide spectral library for better understanding and its efficient usage in DIA database search
ThermoRawFileParser
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
Uniqpepextractor
Tryptic peptides unique to a protein/species from a list of multiple proteins/species fasta files can be extracted.
VarClassFDR
Calculate class FDR for variant peptides identified from Proteome Discoverer results
VFDB_result_fetcher
Genome coordinates can be extracted for the ORFs of virulent factors and the variants of peptides falling within these ORFs can be fetched. Virulent factor class (VFclass), virulence factors and related genes details can be extracted for all the matched variants.