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https://CRAN.R-project.org/package=ComplexUpset
Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.
Proper citation: ComplexUpset (RRID:SCR_022752) Copy
Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets.
Proper citation: UpSet (RRID:SCR_022731) Copy
https://upsetplot.readthedocs.io/en/stable/
Software Python implementation of UpSet plots to visualize set overlaps.
Proper citation: UpSetPlot (RRID:SCR_023225) Copy
http://bioinformatics.fh-hagenberg.at/site/index.php?id=17
Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria.
Proper citation: MS Amanda (RRID:SCR_018396) Copy
https://github.com/Martin-Fahrenberger/GTestimate
Software R package for scRNA-seq normalization. Uses Simple Good-Turing estimator for the per cell relative gene expression estimation.
Proper citation: GTestimate (RRID:SCR_026562) Copy
https://masst.gnps2.org/microbemasst/
Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.
Proper citation: microbeMASST (RRID:SCR_024713) Copy
Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.
Proper citation: IQ-TREE (RRID:SCR_017254) Copy
https://imputationserver.sph.umich.edu/
Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.
Proper citation: Michigan Imputation Server (RRID:SCR_017579) Copy
https://imputationserver.sph.umich.edu/index.html#!pages/home
Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.
Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy
https://data.broadinstitute.org/alkesgroup/Eagle/
Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.
Proper citation: Eagle (RRID:SCR_015991) Copy
https://reprint-apms.org/?q=chooseworkflow
Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.
Proper citation: CRAPome (RRID:SCR_025008) Copy
https://github.com/BGSpiegl/GCparagon
Software Python commandline tool for rapid calculation and correction of fragment length specific GC biases in WGS cfDNA sequencing datasets for liquid biopsy applications. Used for evaluating and correcting GC biases in cell-free DNA at fragment level.
Proper citation: GCparagon (RRID:SCR_026827) Copy
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