Tools   Select Another Resource Report Type

https://www.unileon.es/

Spanish public university with campus in Leon and Ponferrada.

Proper citation: University of Leon, Spain (RRID:SCR_019071) Copy   

•   Source: SciCrunch Registry

http://webapps.embl-hamburg.de/rapido/

Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains.

Proper citation: RAPIDO (RRID:SCR_018935) Copy   

•   Source: SciCrunch Registry

http://xena.ucsc.edu/

Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables.

Proper citation: UCSC Xena (RRID:SCR_018938) Copy   

•   Source: SciCrunch Registry

https://docs.osparc.io

Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response.

Proper citation: o²S²PARC (RRID:SCR_018997) Copy   

•   Source: SciCrunch Registry

https://proteins.plus/

Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported.

Proper citation: Protein.Plus (RRID:SCR_019044) Copy   

•   Source: SciCrunch Registry

https://nrdg.github.io/fracridge

Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.

Proper citation: fracridge (RRID:SCR_019045) Copy   

•   Source: SciCrunch Registry

https://openwetware.org/wiki/RAVE

Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG).

Proper citation: RAVE (RRID:SCR_019040) Copy   

•   Source: SciCrunch Registry

http://cello.life.nctu.edu.tw/cello2go/

Web server for protein subcellular localization prediction with functional gene ontology annotation. Web based system for screening various properties of targeted protein and its subcellular localization.

Proper citation: Cello2Go (RRID:SCR_019042) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.

Proper citation: PROCHECK (RRID:SCR_019043) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/scTHI/

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

Proper citation: scTHI (RRID:SCR_018918) Copy   

•   Source: SciCrunch Registry

https://www.leicabiosystems.com/histology-equipment/tissue-processors/products/leica-asp300-s/

Processor that automatically washes tissue sample which needs to be usable in downstream processes. Designed for routine and research histopathology of up to 300 cassettes.

Proper citation: Leica: ASP300S Fully Enclosed Tissue Processor (RRID:SCR_018916) Copy   

•   Source: SciCrunch Registry

https://mcule.com/

Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties.

Proper citation: Mcule (RRID:SCR_018921) Copy   

•   Source: SciCrunch Registry

https://github.com/najasplus/hetindel_shinyapp

Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.

Proper citation: Hetindel (RRID:SCR_018922) Copy   

•   Source: SciCrunch Registry

http://www.nonlinear.com/progenesis/qi-for-proteomics/

Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.

Proper citation: Progenesis QI (RRID:SCR_018923) Copy   

•   Source: SciCrunch Registry

https://usdrn.org/

Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.

Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy   

•   Source: SciCrunch Registry

http://markummitchell.github.io/engauge-digitizer/

Software tool accepts image files (like PNG, JPEG and TIFF) containing graphs, and recovers the data points from those graphs. Used to convert graphs to data points. Imports image file and then digitizes it by placing points along axes and curves.

Proper citation: Engauge Digitizer (RRID:SCR_019056) Copy   

•   Source: SciCrunch Registry

http://www.cuemol.org/en/

Software tool for macromolecular structure visualization. Molecular visualization framework to visualize crystallographic models of macromolecules. Used to visualize and create publication quality images of macromolecular structures with user friendly interfaces.

Proper citation: CueMol (RRID:SCR_019052) Copy   

•   Source: SciCrunch Registry

https://www.otago.ac.nz/chatterjee-lab/tools/index.html

Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity.

Proper citation: Differential Methylation Analysis Package (RRID:SCR_019148) Copy   

•   Source: SciCrunch Registry

https://github.com/Griffan/FASTQuick

Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation.

Proper citation: FASTQuick (RRID:SCR_019269) Copy   

•   Source: SciCrunch Registry

https://www.nurseshealthstudy.org/

Portal about prospective investigations into risk factors for major chronic diseases in women. Nurses were selected as study population because of their knowledge about health and their ability to provide complete and accurate information regarding various diseases, due to their nursing education.The largest longitudinal study of women. Started in 1976, involving 275000 participants.

Proper citation: Nurses Health Study (RRID:SCR_019144) Copy   

•   Source: SciCrunch Registry