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https://www.sunchrom.de/en/products/maldi-ms-sample-preparation-2/suntissueprep.html
System automates all tissue section preparation steps that were previously performed manually. Deparaffinization, rehydration, antigen-retrieval and pH-adjustment steps are performed efficiently, reliably and fully automated.
Proper citation: SunChrom: SunTissuePrep Tissue Section Preparation System (RRID:SCR_023904) Copy
https://genome.sph.umich.edu/wiki/EMMAX
Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.
Proper citation: EMMAX (RRID:SCR_024012) Copy
https://biocore.github.io/emperor/
Web browser enabled tool with versatile command line interface to perform exploratory investigations of 3D visualizations of microbial community data, such as principal coordinates plots. EMPeror includes set of controllers to modify features as function of metadata. Web interactive next generation tool for analysis, visualization and understanding of high throughput microbial ecology datasets.
Proper citation: EMPeror (RRID:SCR_024013) Copy
https://embossgui.sourceforge.net/
Web based graphical user interface to the EMBOSS suite of bioinformatics tools.
Proper citation: EMBOSS explorer (RRID:SCR_024014) Copy
Leica ST5010 Autostainer XL provides reproducible, consistent high quality staining, and increased workload throughput compared to manual staining.
Proper citation: Leica: Autostainer ST5010 XL (RRID:SCR_023957) Copy
https://www.beckman.com/flow-cytometry/clinical-flow-cytometers/navios-ex
Designed specifically for clinical laboratory NAVIOS EX 10-color flow cytometer delivers performance with improved sample traceability and reporting functions. Navios EX has two optional ready-to-use IVD reagent systems, the Navios Tetra System for simultaneous identification and enumeration of T, B and NK lymphocytes and the ClearLLab 10C System – the first FDA cleared and CE marked integrated leukemia and lymphoma immunophenotyping system.
Proper citation: Beckman Coulter: Navios EX flow cytometer (RRID:SCR_023797) Copy
Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer.
Proper citation: dicompyler (RRID:SCR_024006) Copy
https://github.com/rrwick/Filtlong
Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter.
Proper citation: Filtlong (RRID:SCR_024020) Copy
https://cran.r-project.org/web/packages/foreign/index.html
Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Proper citation: foreign (RRID:SCR_024025) Copy
https://github.com/RobertoDF/BRIO
Software visualization and analysis tool based on the Allen Brain Atlas connectivity database. Produces custom visualizations and figures for input output strength of specific brain area.
Proper citation: BRain area Input Output (RRID:SCR_023846) Copy
https://www.nrel.gov/grid/wind-toolkit.html
United States national wind dataset. Provides high spatial and temporal resolution wind power, wind power forecast, and meteorological data for 7-year period at over 126,000 locations throughout continental United States. The largest publicly available wind power data set in the world. Used for wind energy integration studies. It is accessible through Web-based API.
Proper citation: Wind Integration National Dataset Toolkit (RRID:SCR_023782) Copy
Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR.
Proper citation: CRISPRscan (RRID:SCR_023777) Copy
Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models.
Proper citation: CancerModels.Org (RRID:SCR_023931) Copy
https://pmc.ncbi.nlm.nih.gov/articles/PMC4525701/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products.
Proper citation: Poly Peak Parser (RRID:SCR_023776) Copy
https://github.com/Aswendt-Lab/AIDAhisto
Software atlas based imaging data analysis tool for quantitative mouse brain histology. Can automatically detect cells in histological mouse brain and spinal cord sections of interest.
Proper citation: AIDAhisto (RRID:SCR_023818) Copy
https://mass-spec.stanford.edu/instruments
Agilent 6495C triple quadrupole LC/MS system increases capacity and sensitivity for targeted quantitation applications. Used to investigate more diverse and biologically relevant groups of targeted peptides, small molecules and metabolites in single experiment without compromising sensitivity, quantitative accuracy, or linearity.
Proper citation: Agilent: 6495 Triple Quadrupole LC/MS (RRID:SCR_023937) Copy
https://github.com/rrwick/Deepbinner
Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads.
Proper citation: Deepbinner (RRID:SCR_024001) Copy
Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions.
Proper citation: CTSim (RRID:SCR_024004) Copy
Software application for isothermal titration calorimetry performed on MicroCal PEAQ instrument by Malvern.
Proper citation: Malvern Panalytical MicroCal PEAQ-ITC analysis (RRID:SCR_023795) Copy
https://www.leica-microsystems.com/products/thunder-imaging-systems/p/thunder-imager-3d-live-cell/
Advanced widefield microscope enabling use of 3D specimens with camera based fluorescence microscopes. System ensures low phototoxicity and photobleaching, i.e., higher throughput with optimal conditions.
Proper citation: Leica: Thunder Imager Live Cell system (RRID:SCR_023794) Copy
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