Tools   Select Another Resource Report Type

https://www.mbfbioscience.com/tissue-mapper

Software for comprehensive annotation and delineation of tissue structures by MBF Bioscience. Creates 3D model from image data and annotates regions of interest from customizable ontology list. Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes.

Proper citation: Tissue Mapper (RRID:SCR_017321) Copy   

•   Source: SciCrunch Registry

http://relacs.sourceforge.net/

Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings.

Proper citation: Relacs (RRID:SCR_017280) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/vesselucida360

Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience.

Proper citation: Vesselucida 360 (RRID:SCR_017320) Copy   

•   Source: SciCrunch Registry

http://www.dibsvis.com/biowheel

Software tool for interactive graphs of high dimensional data. Interactive cloud based software tool by DIBSVIS.

Proper citation: BioWheel (RRID:SCR_017441) Copy   

•   Source: SciCrunch Registry

https://github.com/ndierckx/NOVOPlasty

Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data.

Proper citation: NOVOPlasty (RRID:SCR_017335) Copy   

•   Source: SciCrunch Registry

https://github.com/SilverLabUCL/SilverLab-Microscope-Software

Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system.

Proper citation: Silver Lab Microscopy Software (RRID:SCR_017456) Copy   

•   Source: SciCrunch Registry

https://scfind.sanger.ac.uk/

Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed.

Proper citation: Scfind (RRID:SCR_017339) Copy   

•   Source: SciCrunch Registry

https://www.cmrr.umn.edu/downloads/mrspa

Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.

Proper citation: MRspa (RRID:SCR_017292) Copy   

•   Source: SciCrunch Registry

https://kimosys.org

Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community.

Proper citation: Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Glimma.html

Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.

Proper citation: Glimma (RRID:SCR_017389) Copy   

•   Source: SciCrunch Registry

https://github.com/JosephCrispell/homoplasyFinder/wiki

Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R.

Proper citation: HomoplasyFinder (RRID:SCR_017300) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/tdtdecodingtoolbox/

Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.

Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy   

•   Source: SciCrunch Registry

https://icsd.products.fiz-karlsruhe.de/

Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research.

Proper citation: Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) Copy   

•   Source: SciCrunch Registry

https://github.com/ISUgenomics/SequelQC

Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.

Proper citation: SequelQC (RRID:SCR_017279) Copy   

•   Source: SciCrunch Registry

https://www.qtiplot.com/

Software tool for data analysis and scientific visualization by IONDEV SRL.

Proper citation: QtiPlot (RRID:SCR_017311) Copy   

•   Source: SciCrunch Registry

https://hnn.brown.edu/

Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data.

Proper citation: Human Neocortical Neurosolver (RRID:SCR_017437) Copy   

•   Source: SciCrunch Registry

https://4dgenome.research.chop.edu/

Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community.

Proper citation: 4D Genome (RRID:SCR_017489) Copy   

•   Source: SciCrunch Registry

http://www.infolanka.com/org/twin-registry/

Independent academic and research institution to establish registration for twins in Sri Lanka , to facilitate study of twins. Center for twin, sibling, family and genetic studies for South Asian Region.

Proper citation: National Twin Registry of Sri Lanka (RRID:SCR_017481) Copy   

•   Source: SciCrunch Registry

https://matr.vcu.edu/about/

Core scientists collaborate with research teams from a variety of disciplines and institutions. MATR services include recruitment, data and sample collection, dataset curation and access, protocol development, cost estimates, grant development support, and IRB submissions. Twins and their families who are willing to consider taking part in twin-based, health-related research can participate. For twins of any age, ethnicity, and zygosity (identical or fraternal), as well as higher order multiples such as triplets, quadruplets and quintuplets. Most of twins registered in MATR are from Virginia, North Carolina, and South Carolina, but twins from all over the country and all around the world are welcome to register. MATR repository containing DNA samples provided by twins and allows to study twin data collected by studies along with their DNA.

Proper citation: Virginia Commonwealth University Mid-Atlantic Twin Registry MATR Core Facility (RRID:SCR_017484) Copy   

•   Source: SciCrunch Registry

http://www.ariesepigenomics.org.uk/

Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.

Proper citation: Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) Copy   

•   Source: SciCrunch Registry