EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

QUANtification by Distillation for ENhanced Signals with Error Regulation

Java implementation of the Aho-Corasick algorithm for efficient string matching

RNA-seq aligner

Tools for handling Unique Molecular Identifiers in NGS data sets

PDV: an integrative proteomics data viewer

An tandem mass spectrometry (MS/MS) sequence database search tool.

A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics

PepQuery: a targeted peptide search engine

Proteomics search & quantification so fast that it feels like magic

😎 A curated list of GitHub badges for your next project

Precision HLA typing from next-generation sequencing data

Semi-supervised learning for peptide identification from shotgun proteomics datasets

A cross-platform proteomics data analysis suite

AutoRT: Peptide retention time prediction using deep learning

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

Customized protein database construction

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Proteogenomic Analysis of a Korean Cohort Reveals Lung Cancer Subtypes Predictive of Metastasis, Chromosome Instability, and Tumor Microenvironment

NeoFlow: a proteogenomics pipeline for neoantigen discovery

Highly adaptable common interface for proteomics search and de novo engines

BamQuery provides RNA-seq quantification for a given peptide (from 8 to 11 residues) in chosen RNA-seq samples (single or bulk).

De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments

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

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.