FHOOE Hagenberg Bioinformatics/Proteomics Research Group
Repositories list
36 repositories
sciex2mgf
PublicREAD
PublicTMTpro-18plex quantification for [single cell] DIA and DDA searches with Chimerys, Spectronaut, and DIA-NN.python-pkg_template
Public templatepython_template
Public templatepyXLMS-manuscript
PublicResults, figures, and code for the manuscript of pyXLMS.READ-GUI
PublicBuild scripts for the Gooey-based GUI version of READ.pyXLMS
PublicA python package to process protein cross-linking data.pyXLMS-template
Public templateA template repository for python scripts and projects using pyXLMS.MSAndrea
Publicr_template
Public templateInternal_Ions_Explorer
PublicpyXLMS-pydantic
Public archivePydantic version of pyXLMS [merged into main pyXLMS in v2.0.0]MSAnnika
PublicMS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra.pyXLMS-docs
PublicA comprehensive user guide for pyXLMS built with Nextra.- Generate a spectral library for Spectronaut from MS Annika results.
- Rescoring of Spectronaut Crosslinking Results with Mokapot.
MSAmanda
PublicMS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.Crosslink_Utils
PublicHelper scripts for crosslink analysis.pyXLMS-app
PublicLink to the web application for pyXLMS.TMT_Resolution_GUI
PublicExtracts TMT reporter ion intensity, noise, and resolution from the corresponding mass spectra.MSAnnika_Extensions
PublicList of all available extensions for our cross-linking search engine MS Annika.MSAnnika_exporters
Public archiveExport MS Annika crosslink results to different formats.exploring_scplainer
PublicSCOmics-Preliminary
PublicMSAnnika_CSM_Annotation
PublicCalculates Intensities of Cross-linked Peptides from MS Annika CSMs.CandidateVectorSearch_template
Public archiveTemplate repository for custom backends in MS Annika.CandidateVectorSearch
Public archiveSearching for peptide candidates using sparse matrix + matrix/vector multiplication.CandidateSearch
Public archiveProof-of-concept implementation of a search engine that uses sparse matrix multiplication to identify the best peptide candidates for a given mass spectrum.MSAnnika_NC_Results
Public archiveRepository containing scripts used for the analysis and visualization of the results of the MS Annika 3.0 non-cleavable crosslink search.
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