compomics/psm_utils

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

Language: Python - Size: 104 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 20 - Forks: 6

compomics/ms2rescore

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

Language: Python - Size: 303 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 38 - Forks: 15

BioGenies/peptide-prediction-list

Collects software dedicated to predicting specific properties of peptides

Language: Shell - Size: 17.5 MB - Last synced: about 15 hours ago - Pushed: over 1 year ago - Stars: 41 - Forks: 8

pgarrett-scripps/peptacular

A spectacularly simple package for working with peptide sequences.

Language: Python - Size: 11.3 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 8 - Forks: 0

LindsayXX/Applied-Bioinformatics

Labs and project archive for DD2404 Applied Bioinformatics

Language: Python - Size: 5.97 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

pgarrett-scripps/PeptideFragmenterStreamlitApp

A peptide fragment ion calculator made with streamlit

Language: Python - Size: 110 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

pgarrett-scripps/ProteinCleaverStreamlitApp

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

Language: Python - Size: 748 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

ursgal/ursgal

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

Language: Python - Size: 13.1 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 41 - Forks: 32

lemieux-lab/pepid

Highly customizable research-oriented peptide search engine

Language: Python - Size: 800 KB - Last synced: 4 days ago - Pushed: 6 months ago - Stars: 2 - Forks: 0

thilus/ms-tagger

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

Language: Java - Size: 4.54 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

denisbeslic/denovopipeline

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

Language: Python - Size: 264 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 22 - Forks: 6

bzhanglab/DeepRescore

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

Language: Nextflow - Size: 77.3 MB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 3

cpanse/protViz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Language: R - Size: 2.42 MB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 10 - Forks: 3

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

Language: Shell - Size: 121 KB - Last synced: 3 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

bzhanglab/PepQuery

PepQuery: a targeted peptide search engine

Language: Java - Size: 321 KB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 0

novak-jiri/cyclobranch

A tool for mass spectrometry data analysis.

Language: C++ - Size: 5.27 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 7 - Forks: 3

pFindStudio/pFind3

Size: 34.2 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 22 - Forks: 7

nh2tran/DeepNovo

Protein Identification with Deep Learning

Language: Python - Size: 174 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 86 - Forks: 39

Arsh25/proteomics

Toolset to make proteomics data analysis less tedious.

Language: Python - Size: 16.1 MB - Last synced: 9 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 0

yufongpeng/PeptideSeq.jl

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

Language: Julia - Size: 2.98 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

fcyu/ECL

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

Language: Java - Size: 105 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 1

fcyu/ECL2

A fast and exhaustive cross-linked peptides identification tool.

Language: Java - Size: 359 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

mellieho9/Antimicrobial-Peptide-Prediction

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

Language: Python - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

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.

Language: R - Size: 1.73 MB - Last synced: 16 days ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

fcyu/PIPI

PTM-Invariant Peptide Identification. An open search tool.

Language: Java - Size: 735 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 5 - Forks: 4

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

Language: Python - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0

fcyu/ECLViewer2

A GUI to view the annotated spectra identified by ECL2

Language: C# - Size: 313 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0