R toolkit for single cell genomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common t…

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Fast and flexible semi-supervised learning for peptide detection in Python

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Tool for the Quality Control of Long-Read Defined Transcriptomes

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

DecoyPYratPlus - Decoy Sequence Database Creation for Proteomic Mass Spectrometery Analyses

Long-read splice alignment with high accuracy

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

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

A OneNote add-in with simple, yet powerful and useful features

Proteomics search & quantification so fast that it feels like magic

Long-read Sequencing Uncovers Novel Alternative Splicing Networks Governing Neuroimmune in an Allergic Rhinitis Mouse model

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

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

ShinyCell2 is a lightweight R package for building interactive, shareable apps to explore single-cell multi-omics, scATAC-seq and spatial transcriptomics data with customizable, publication-ready v…

Directly selecting cell-type marker genes for single-cell clustering analyses

MSigDB gene sets for multiple organisms in a tidy data format

Distributed NMF/NTF Library