peptide-identification

BioGenies/peptide-prediction-list

Collects software dedicated to predicting specific properties of peptides

compomics/ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

ursgal/ursgal

Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis

MannLabs/alphadia

modular & open DIA search

compomics/ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

denisbeslic/denovopipeline

Pipeline for de novo peptide sequencing (Novor, DeepNovo, SMSNet, PointNovo, Casanovo) and assembly with ALPS.

compomics/psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

pFindStudio/pFind3

cpanse/protViz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

novak-jiri/cyclobranch

A tool for mass spectrometry data analysis.

bzhanglab/PepQuery

PepQuery: a targeted peptide search engine

pgarrett-scripps/peptacular

A spectacularly simple package for working with peptide sequences.

bzhanglab/DeepRescore

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

fcyu/PIPI

PTM-Invariant Peptide Identification. An open search tool.

BioGenies/CancerGram

Predicts anticancer peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI.

pgarrett-scripps/ProteinCleaverStreamlitApp

Protein Cleaver is a versatile tool for protein analysis and digestion.

dusteenie/Genome-Data-Quality-Control

This repository contains scripts used to clean genome sequencing data; such that it passes quality control for analysis. Script(s) include: Open Reading Frame. Code is written in Python 3. Spring 2021

fcyu/ECL

This project has been deprecated. Please use ECL2 (https://github.com/fcyu/ECL2).

fcyu/ECL2

A fast and exhaustive cross-linked peptides identification tool.

lemieux-lab/pepid

Highly customizable research-oriented peptide search engine

pgarrett-scripps/PeptideFragmenterStreamlitApp

A peptide fragment ion calculator made with streamlit

Arsh25/proteomics

Toolset to make proteomics data analysis less tedious.

AstraBert/PredGenesGetPepts

PredGenesGetPepts is an easy-to-use, beginner-friendly pipeline to call genes from fasta files, retrieve peptides and blasting them against a given protein database

hgb-bin-proteomics/CandidateSearch

Proof-of-concept implementation of a search engine that uses sparse matrix multiplication to identify the best peptide candidates for a given mass spectrum.

hgb-bin-proteomics/MSAmanda

MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.

mellieho9/Antimicrobial-Peptide-Prediction

A bioinformatics project to predict antimicrobial peptides using Pfeature, CD-HIT, and Random Forest Generation

yufongpeng/PeptideSeq.jl

Predict and match digested peptides sequences, their mass m/z and MS/MS spectra with chemical derivatization or post-translational modification.

fcyu/ECLViewer2

A GUI to view the annotated spectra identified by ECL2

LindsayXX/Applied-Bioinformatics

Labs and project archive for DD2404 Applied Bioinformatics

thilus/ms-tagger

Graph-based algorithm for generating peptide tags from MS/MS data

BioGenies/kmerFilters

Tools for filtering k-mer data

hgb-bin-proteomics/CandidateVectorSearch

Searching for peptide candidates using sparse matrix + matrix/vector multiplication.

hgb-bin-proteomics/CandidateVectorSearch_template

Template repository for custom backends in MS Annika.