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https://github.com/SGDDNB/ShinyCell

Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data.

Proper citation: ShinyCell (RRID:SCR_022756) Copy   

•   Source: SciCrunch Registry

https://www.licor.com/bio/odyssey-xf/

System includes Odyssey XF Imager and Empiria Studio Software for streamlined image acquisition, organization, and analysis of Western blots. Used for imaging near infrared and enhanced chemiluminescent Western blots, to detect multiple targets on same blot with two channel multiplex fluorescence, and document DNA gels.

Proper citation: LI-COR: Odyssey XF Imaging System (RRID:SCR_022510) Copy   

•   Source: SciCrunch Registry

https://www.antibodysociety.org/the-airr-community/

Research driven group that is organizing and coordinating stakeholders in use of next generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. Develops and promotes standards and recommendations for obtaining, analyzing, curating and comparing/sharing AIRR-seq datasets;using and validating tools for analyzing AIRR-seq data;relating AIRR-seq datasets to other “big data” sets, such as microarray, flow cytometric, and MiSeq and single-cell gene-expression data; legal and ethical issues involving use and sharing of AIRR-seq data sets derived from human sources.

Proper citation: AIRR Community (RRID:SCR_022598) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://zdock.umassmed.edu/

Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers.

Proper citation: ZDOCK Server (RRID:SCR_022518) Copy   

•   Source: SciCrunch Registry

https://github.com/Gaius-Augustus/learnMSA

Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded.

Proper citation: learnMSA (RRID:SCR_022572) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionLab/sei-framework

Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.

Proper citation: sei (RRID:SCR_022571) Copy   

•   Source: SciCrunch Registry

https://github.com/djamesbarker/pMAT

Open source software suite for analysis of fiber photometry data.

Proper citation: pMAT (RRID:SCR_022570) Copy   

•   Source: SciCrunch Registry

https://github.com/JinmiaoChenLab/Rphenograph

Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.

Proper citation: Rphenograph (RRID:SCR_022603) Copy   

•   Source: SciCrunch Registry

https://www.ibm.com/products/structural-equation-modeling-sem

Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance.

Proper citation: IBM SPSS Amos (RRID:SCR_022686) Copy   

•   Source: SciCrunch Registry

https://quality-preclinical-data.eu/about-eqipd/eqipd-quality-system/

Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD.

Proper citation: Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) Copy   

•   Source: SciCrunch Registry

https://www.rcon-ndt.com/products/radiography/x-ray-systems/phoenix-nanotom-s/

Nanofocus computed tomography system for applications in material science, precision injection moulding, micromechanics, electronics geology and biology. System includes nanofocus X-ray tube, precision mechanics and advanced software modules. Used for range of 3D CT applications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GE: Phoenix Nanotom S system (RRID:SCR_022582) Copy   

•   Source: SciCrunch Registry

http://splicing.cs.washington.edu/

Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events.

Proper citation: Hexamer Additive Linear (RRID:SCR_022581) Copy   

•   Source: SciCrunch Registry

https://web.rniapps.net/netshift/

Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets.

Proper citation: NetShift (RRID:SCR_022733) Copy   

•   Source: SciCrunch Registry

https://www.fishersci.com/shop/products/cryostar-nx50-cryostat-1/957130

Manual cryostat designed to accommodate needs of routine clinical laboratory by offering form fitting ergonomic design, with optional height adjustment, vacutome and cold D disinfection.

Proper citation: Epredia: CryoStar NX50 Cryostat (RRID:SCR_022732) Copy   

•   Source: SciCrunch Registry

https://upset.app/#:~:text=UpSet%20plots%20the%20intersections%20of,is%20part%20of%20an%20intersection.

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   

•   Source: SciCrunch Registry

http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/

Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses.

Proper citation: VirtualPlant (RRID:SCR_022576) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/A24811

Bentchtop Thermal Cycler for everyday PCR. Features innovative, safe heated lid and large LCD color touch screen.

Proper citation: Thermo Fisher: Applied Biosystems: SimpliAmp Thermal Cycler (RRID:SCR_023004) Copy   

•   Source: SciCrunch Registry

https://biccn.org/teams/u01-fischl

Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex.

Proper citation: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain (RRID:SCR_023000) Copy   

•   Source: SciCrunch Registry

https://www.internationalbrainlab.com/data

Data portal hosting access to behavioral data sets generated by International Brain Laboratory aiming to understand brain functions underlying decision making. Datasets are acquired in neuroscience laboratories performing experimental work. In each of these laboratories, mice are first trained in IBL decision making task following standardized training pipeline.

Proper citation: International Brain Laboratory Data (RRID:SCR_022946) Copy   

•   Source: SciCrunch Registry