Miscellaneous Scripts in Bioinformatics

Tools for filtering k-mer data

Template repository for custom backends in MS Annika.

A GUI to view the annotated spectra identified by ECL2

Labs and project archive for DD2404 Applied Bioinformatics

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

Toolset to make proteomics data analysis less tedious.

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

Proteomics Identifications & Quantitations Data Management & Integration Service

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

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

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

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

A peptide fragment ion calculator made with streamlit

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

Highly customizable research-oriented peptide search engine

A fast and exhaustive cross-linked peptides identification tool.

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

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

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