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Name: Chinmaya Narayana
Type: User
Company: Yenepoya Research Centre
Bio: Research Graduate, Center for Systems Biology and Molecular Medicine, Yenepoya, Mangaluru, India
Location: Mangaluru
Name: Chinmaya Narayana
Type: User
Company: Yenepoya Research Centre
Bio: Research Graduate, Center for Systems Biology and Molecular Medicine, Yenepoya, Mangaluru, India
Location: Mangaluru
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)
A list of tools on proteomics using deep learning
Extract the identified peptides and proteins from spectral library search of DIA proteomic data in Skyline
Identification, Counting the number of rows and Deleting of files based on suffix, prefix or other search terms in multiple directories
Extract raw file specific spectra from an unassigned spectra file (.mgf) from Proteome Discoverer and generate new .mgf files specific to raw files
Generate annotated Peptide Spectrum Matches (PSMs) from proteomic database search result
Python packages for easy execution of proteogenomic workflow
python scripts for proteogenomics analysis
A proteogenomics approach to identify cancer variants and neoantigens
Validation of modified amino acid sites in peptide sequences by identifying immonium ions in the raw spectra (.mgf format)
Summarize post-translationally modified amino acid sites, peptides and proteins for Proteome Discoverer output
Python tools for proteogenomics analysis toolkit
Scripts used for proteomic data formatting and extraction
Routinely used R scripts in statistical analysis of proteomic experiment results with figure and plot generation
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
Calculate Normalized Spectral Contrast Angle Score for Peptide Spectrum Matches (PSMs) using Prosit predicted peptide library
Extracts the features of peptide spectral library for better understanding and its efficient usage in DIA database search
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
LC-MS/MS derived peptide retention time deviation calculator across replicates for DDA and DIA derived result files.
Tryptic peptides unique to a protein/species from a list of multiple proteins/species fasta files can be extracted.
Calculate class FDR for variant peptides identified from Proteome Discoverer results
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.
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.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
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Data-Driven Documents codes.
China tencent open source team.