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https://blobtoolkit.genomehubs.org/blobtools2/

Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.

Proper citation: BlobTools2 (RRID:SCR_023351) Copy   

•   Source: SciCrunch Registry

https://www.diagenode.com/en/categories/bioruptor-shearing-device

Sonication system for optimal shearing of biological and chemical samples.

Proper citation: Diagenode: Bioruptor (RRID:SCR_023470) Copy   

•   Source: SciCrunch Registry

https://rth.dk/resources/risearch/

Software tool for prediction of RNA–RNA, RNA–DNA, and DNA–DNA interactions. Both RIsearch1 and RIsearch2 enable quick localisation of potential near complementary interactions between given query and target sequences. RIsearch1 performs computation with whole sequences. RIsearch2 focuses on perfect complementary seed regions and extends them on both ends. User defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (e.g., siRNA and Cas9–gRNA off-target predictions).

Proper citation: RIsearch (RRID:SCR_023503) Copy   

•   Source: SciCrunch Registry

https://www.promega.com/resources/software-firmware/glomax-systems/glomax-discover-system-software/

System includes firmware and plate reader software for reading absorbance, fluorescence, or luminescence in 96-well plates.

Proper citation: GloMax Discover System Software and Firmware (RRID:SCR_023469) Copy   

•   Source: SciCrunch Registry

https://kosis.kr/

Republic of Korea e-Government platform for major domestic, international and North Korean statistics. Web service provides official statistics produced by statistical agencies covering more than 500 subject matters as well as the latest data on international finance and economy from international organizations i.e. IMF, World Bank, OECD.

Proper citation: Korea Statistical Information Service (RRID:SCR_023565) Copy   

•   Source: SciCrunch Registry

https://omsf.io/

Nonprofit organization with mission to advance molecular sciences by building open source software and sustainable communities for research software development. Focuses on working with hosted projects to support their software development and provide operational support, while also pursuing own community-service and community-building projects. Uses fiscal sponsorship as business model available to nonprofit organizations to assemble resources, provide support and advance open source projects in molecular sciences aligned with charitable purpose and general public interest.

Proper citation: Open Molecular Software Foundation (RRID:SCR_023440) Copy   

•   Source: SciCrunch Registry

https://github.com/lucadellasantina/ObjectFinder

Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes.

Proper citation: ObjectFinder (RRID:SCR_023319) Copy   

•   Source: SciCrunch Registry

https://neuromorpho.org/xyz2swc/ui/

Web service that converts all 30 reconstruction formats (and 65 variations) described in scientific literature into SWC standard. Service is available open-source through user-friendly browser interface and Application Programming Interface.

Proper citation: xyz2swc (RRID:SCR_023317) Copy   

•   Source: SciCrunch Registry

https://github.com/PedroBarbosa/DeepIntronic_Benchmark

Repository of code, data, and documentation to reproduce computational evaluation performed to identify the best tools/models to predict genetic variation in deep intronic regions of human genome.

Proper citation: Benchmark of human deep intronic variation (RRID:SCR_023315) Copy   

•   Source: SciCrunch Registry

https://github.com/PedroBarbosa/VETA

Software tool that analyses performance of several variant prediction methods at different levels. Used to benchmark variant effect predictors from VCF files.

Proper citation: Variant Prediction Tools Evaluation (RRID:SCR_023314) Copy   

•   Source: SciCrunch Registry

https://precisionhealth.umich.edu/our-research/michigangenomics/

Collaborative research effort among physicians, researchers, and patients at the University of Michigan with goal of combining patient electronic health record data with corresponding genetic data to gain novel biomedical insights. Biobank linking genotypes and electronic clinical records in Michigan Medicine patients. MGI participants agree to provide study team with access to EHR data for clinical information and biospecimen including blood or saliva.

Proper citation: Michigan Genomics Initiative (RRID:SCR_023556) Copy   

•   Source: SciCrunch Registry

https://github.com/frlender/DendroX

Web application for multi-level multi-cluster selections in dendrogram. Provides interactive visualization of dendrogram in which users can divide dendrogram at any level and into any number of clusters.

Proper citation: DendroX (RRID:SCR_023434) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/roifile/

Software Python package to read, write, create, and plot ImageJ ROI format, an undocumented and ImageJ application specific format to store regions of interest, geometric shapes, paths, text, and whatnot for image overlays.

Proper citation: roifile (RRID:SCR_023331) Copy   

•   Source: SciCrunch Registry

https://www.gmi-inc.com/product/nuaire-labgard-es-nu-425-biosafety-cabinet-series-2/

Designed for laboratory safety, proper ergonomics, and energy efficiency.Models available from GMI are 2-ft. NU-425-200, 3-ft. NU-425-300, 4-ft. NU-425-400, and 6-ft. NU-425-600. LabGard NU-425 biosafety cabinets feature control system to control blower, lights, and outlets, Minihelic gauge that measures plenum performance, and Attenumount vibration control system for attenuation of sound and vibration. Cabinets are equipped with highly efficient, energy-saving motor/blower to increase filter life and cut electricity costs.

Proper citation: NuAire: LabGard ES NU-425-600E Biosafety Cabinet (RRID:SCR_023448) Copy   

•   Source: SciCrunch Registry

https://www.perkinelmer.com/product/harmony-5-1-office-hh17000012

Software tool designed by PerkinElmer for high content screening systems. Used to quantify complex cellular phenotypes. High content analysis software.

Proper citation: Harmony (RRID:SCR_023543) Copy   

•   Source: SciCrunch Registry

https://www.fasteris.com/en-us/NGS

Fasteris, the brand of Genesupport SA for all Life Science Services, provides Next Generation Sequencing and Sanger sequencing services.Offers customized approaches and consulting services at each step of your projects.

Proper citation: Fasteris Next Generation Sequencing Services (RRID:SCR_023421) Copy   

•   Source: SciCrunch Registry

https://www.gehealthcare.com/products/advanced-visualization/all-applications/volume-viewer

Software tool to provide data 3D visualization and processing. Used for reading and comparing CT, MR, 3D X-ray, PET, and PET/CT datasets.

Proper citation: GE Volume Viewer (RRID:SCR_023417) Copy   

•   Source: SciCrunch Registry

https://www.fz-juelich.de/en

One of the largest interdisciplinary research centers in Europe for inspiring science exchange from all over the world. It is member of the Helmholtz Association.

Proper citation: Research Center Jülich; Jülich; Germany (RRID:SCR_023416) Copy   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/SlideSeq_Pipeline/README/

Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay.

Proper citation: Slide-seq Pipeline (RRID:SCR_023379) Copy   

•   Source: SciCrunch Registry

https://github.com/CaT-zTools/CaT-z_Software

Software tool for 3D tracking and automatic classification of rodent behavior. Used for acquisition, annotation, and automatic behavioral profile characterization of laboratory rodents' RGB-D videos. Utilizes video segmentation, tracking of body parts, and automated classification of behaviors through machine learning and computer vision methods. Setup uses low costing RGB-D cameras for tracking behaviors in various environments. Software includes GUI interfaces for video acquisition, annotation, and processing of behavioral data. Software is capable of automated behavior detection with only 30 minutes of annotated video.

Proper citation: CaT-z (RRID:SCR_023399) Copy   

•   Source: SciCrunch Registry