SaeedLab/SpectraVision

Identifiers in the GTN correspond to training materials in various formats (markdown, slides, video). The users can apply learned concepts directly within the framework via galaxy workflows.

High-performance open-source proteomics database search engine written in Rust, converting raw mass spectra into peptide identifications via fragment-indexed searching with machine-learned PSM rescoring (LDA), retention-time prediction, chimeric/co-fragmenting spectrum search, and TMT/label-free quantification at scale; cloud-native with S3/GCS/Azure streaming, Percolator/Mokapot-compatible output, and integration into quantms and OpenMS pipelines, widely adopted in AI-driven proteomics workflows (312+ stars, MIT License, actively maintained)

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.

This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.

Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

A client to simplify fetching predictions from the Koina web service. Koina is a model repository enabling the remote execution of models. Predictions are generated as a response to HTTP/S requests, the standard protocol used for nearly all web traffic.