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brenda-parse

Simple python script for parsing BRENDA enzyme database into a table containing:

calisp

Isope Analysis of Proteomics Data

chew

CHEW: Accessible metagenome free metaproteomics analysis

de-novo-errorsim

Simulation of de novo errors for modelling proteomics

deepnovo-mgf-fileprep

2 python scripts and one bash for prepping raw files to deepnovo MGF format, and using idXML to add sequence information for training your own datasets.

fragment_predictor

Predicts all peptide fragments for a peptide. Based on "Expert Systems"

gtdb2diamond

Set of simple auxiliary python scripts to help create GTDB databases for annotation with DIAMOND

gtdb2qiime

Python scripts to parse GTDB ssu fna files to a format useable by Qiime, for taxonomic annotation with classifiers.

gtdb_uniprot_busco

Script to generate a homogenized GTDB database from taxa in UniprotKB reference proteomes

idxml2psms

single python script to convert .idXML files to PMSs format, which is generated by proteome discoverer. This particular pipeline was used to generate PSMs outputs for Calisp2 without needing to use proteome discoverer.

kegg-parse

compilation of scripts used to parse kegg information to tables

ms-feature_exctraction

Scripts for recalibrating MS1/MS2 mzml files from proteomics or metabolomics data

ncbi2lineage

Single python script to construct lineages from ncbi taxdump files names.dmp and nodes.dmp.

novobridge

novobridge_plus

update of NovoBridge with miscleavage handling and multiple candidate submission

novolign

proteomic-database-prepper

this is a small auxiliary python script that helps with preparing proteomic databases for annotation.

pyhton_metaprosip

Python wrapped openMS pipeline from KNIME for SIP analysis in metaproteomics. In this case MSGF is changed to MSFragger for faster spectrum matching.

sippy

Python workflow for stable isotope incorporation proteomics

tofsims-grd

Scripts for processing raw data format TOF SIMS data

unimod_parse

Very simple script to download and parse the delta mass shift and composition shift of unimod modifications

uniprotkb-function-scrape

The new UniprotKB website has very limited query size in API, and prevents downloading customized slices of UniprotKB for functional mapping.

uniref2lineage

A python script to support UniprotKB mapping from uniref accessions to uniprot accessions and uniprot metadata, such as lineages go terms and enzyme classification numbers.

useful_visualizations