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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

https://pypi.org/search/?q=EmaCalc

Software package in Python for statistical analysis of Ecological Momentary Assessment data.

Proper citation: EmaCalc (RRID:SCR_022943) Copy   

•   Source: SciCrunch Registry

https://mriqc.readthedocs.io/en/latest/

Software tool as quality assurance workflow for Brain Imaging Data Structure compliant anatomical and functional MRI datasets. Used to extract no-reference image quality metrics from structural and functional magnetic resonance imaging data.

Proper citation: MRIQC (RRID:SCR_022942) Copy   

•   Source: SciCrunch Registry

https://cytotrace.stanford.edu/

Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data.

Proper citation: CytoTRACE (RRID:SCR_022828) Copy   

•   Source: SciCrunch Registry

http://www.ohsu.edu/xd/education/schools/school-of-medicine/academic-programs/neuroscience-graduate-program//

The Neuroscience Graduate Program (NGP) at OHSU provides outstanding, multidisciplinary training in neuroscience in one of the best-recognized neuroscience programs in the United States. Our graduates are distributed at top research institutions throughout the world, and the success of our faculty ensures that graduates have ready access to their next step ����?? be it postdoctoral fellowships in academia or industry, or other science-related careers. The program is particularly strong in cellular neuroscience, neuronal signaling, gene regulation, biophysics of channels and transporters, sensory systems, and neuroendocrinology with increasing strength in developmental neuroscience and disease-oriented neuroscience research. Faculty members are located within research institutes at OHSU including the Vollum Institute, the Oregon National Primate Research Center (ONPRC), Oregon Hearing Research Center, Jungers Center and the Center for Research on Occupational and Environmental Toxicology (CROET); as well as the basic and clinical departments in the OHSU School of Medicine. As time spent in the lab is the most important component of graduate science training, our program is designed such that core coursework is completed in the first year. During that first year, students also are immersed in research through lab rotations in several labs, eventually choosing one that gives a mutual fit. Because of the relatively small number of students compared to the number of neuroscience laboratories at OHSU, students have many options for a thesis lab. Our well funded faculty provide state-of-the-art exposure to the concepts and technology of modern neuroscience. OHSU also offers certificate and degree programs, e.g. technology transfer and translational science, for advanced students in the NGP who want to broaden their career options.

Proper citation: Oregon Health and Science University Neuroscience Graduate Program (RRID:SCR_003508) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/

Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization.

Proper citation: Plant mPLoc (RRID:SCR_023014) Copy   

•   Source: SciCrunch Registry

https://abi-services.informatik.uni-tuebingen.de/multiloc2/webloc.cgi

Web application for integrating phylogeny and Gene Ontology terms into subcellular protein colalization prediction.Extensive high performance subcellular protein localization prediction system.

Proper citation: Multi Loc2 (RRID:SCR_023013) Copy   

•   Source: SciCrunch Registry

https://www.vosesoftware.com/products/modelrisk/

Monte Carlo simulation software that makes quantitative risk analysis intuitive. Monte Carlo simulation Excel add-in that allows user to include uncertainty in their spreadsheet models.

Proper citation: ModelRisk (RRID:SCR_022836) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pi-usb-cam/

Project related to video recording.Provides system for high throughput video capture. Pi USB Cam system includes low cost Raspberry Pi microcomputer, DIY electronics peripherals, freely available open-source firmware, and custom 3D-printed casings.

Proper citation: Pi USB Cam project (RRID:SCR_022834) Copy   

•   Source: SciCrunch Registry

https://qdr.syr.edu/

Archive for storing and sharing digital data (and accompanying documentation) generated or collected through qualitative and multi method research in social sciences. QDR provides data management consulting services and actively curates all data projects, maintaining value and usefulness of data over time, and ensuring their availability and findability for re-use.

Proper citation: Qualitative Data Repository (RRID:SCR_022833) Copy   

•   Source: SciCrunch Registry

https://github.com/schneebergerlab/syri

SyRI compares alignments between two chromosome level assemblies and identifies synteny and structural rearrangements.

Proper citation: SyRI (RRID:SCR_023008) Copy   

•   Source: SciCrunch Registry

https://github.com/Malindrie/scShapes

Software tool as statistical framework for identifying distribution shapes in single-cell RNA-sequencing data.

Proper citation: scShapes (RRID:SCR_022838) Copy   

•   Source: SciCrunch Registry

https://www.palisade.com/risk/

Software is add-in tool for Microsoft Excel that computes and tracks many different possible scenarios in model using Monte Carlo simulation.Helps make better decisions through risk modeling and analysis.

Proper citation: atRISK (RRID:SCR_022837) Copy   

•   Source: SciCrunch Registry

https://www.radiantviewer.com/products/radiant-dicom-viewer-standard/

Software tool as Digital Imaging and Communications in Medicine (DICOM) viewer for medical images.

Proper citation: RadiAnt DICOM Viewer (RRID:SCR_022894) Copy   

•   Source: SciCrunch Registry

https://github.com/bulik/ldsc/wiki

Command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.

Proper citation: LDSC (RRID:SCR_022801) Copy   

•   Source: SciCrunch Registry

https://www.visualsonics.com/product/imaging-systems/vevo-770

High resolution in vivo imaging system for small animal research. Provides visualization and measurement of anatomical and hemodynamic function in small animals down to 30 microns.

Proper citation: Fujifilm: VisualSonics Vevo 770 Imaging System (RRID:SCR_022921) Copy   

•   Source: SciCrunch Registry