chinmayaNK22

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

MS-noise-eraser

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

py-pgatk

Python tools for proteogenomics analysis toolkit

Python-Scripts

Scripts used for proteomic data formatting and extraction

R_Scripts

Routinely used R scripts in statistical analysis of proteomic experiment results with figure and plot generation

Sixframe

This program helps to perform six frame translation of the genome provided. For the proteogenomics analysis, this also allows to prepocess and remove certain sequences before PD search

SpecAngle

Calculate Normalized Spectral Contrast Angle Score for Peptide Spectrum Matches (PSMs) using Prosit predicted peptide library

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

UniformRT

LC-MS/MS derived peptide retention time deviation calculator across replicates for DDA and DIA derived result files.

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.