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http://bioconductor.org/packages/release/bioc/html/MetaCyto.html

Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.

Proper citation: MetaCyto (RRID:SCR_016415) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/vpv

Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph.

Proper citation: VPV (RRID:SCR_016545) Copy   

•   Source: SciCrunch Registry

https://cm.jefferson.edu/rna22/

Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.

Proper citation: RNA22 (RRID:SCR_016507) Copy   

•   Source: SciCrunch Registry

https://www.uamh.ca/

Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi.

Proper citation: UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) Copy   

•   Source: SciCrunch Registry

http://gcm.wfcc.info/

Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.

Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy   

•   Source: SciCrunch Registry

http://grey.colorado.edu/emergent

emergent is a comprehensive, full-featured neural network simulator that allows for the creation and analysis of complex, sophisticated models of the brain in the world. With an emphasis on qualitative analysis and teaching, it also supports the workflow of professional neural network researchers. Its high level drag-and-drop programming interface, built on top of a scripting language that has full introspective access to all aspects of networks and the software itself, allows one to write programs that seamlessly weave together the training of a network and evolution of its environment without ever typing out a line of code. Networks and all of their state variables are visually inspected in 3d, allowing for a quick visual regression of network dynamics and robot behavior. This same 3d world sports a highly accurate Newtonian physics simulation, allowing you to create rich robotics simulations (for example, a car). As a direct descendant of PDP (1986) and PDP (1999), emergent has been in development for decades. In the most recent versions available strive to distill it down to its essential elements. Those that take the time to learn the best practices will be rewarded with the ability to create and understand the most complicated neural models ever published.

Proper citation: Emergent (RRID:SCR_008500) Copy   

•   Source: SciCrunch Registry

http://www.neuroscience.cam.ac.uk/

This portal provides information about the neuroscience department at the University of Cambridge. Cambridge has a strong tradition in neuroscience having been host to the first analyses of neural signaling in the 1930s, determined the mechanisms of neuronal firing in the 1950s, and heralded some of the early theoretical approaches to the functions of neural circuitry in the 1960s. Neuroscience continues to grow at Cambridge, with an impressive record of achievement in multidisciplinary research.

Proper citation: Cambridge Neuroscience Department (RRID:SCR_008649) Copy   

•   Source: SciCrunch Registry

http://apid.dep.usal.es

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

Proper citation: Agile Protein Interactomes DataServer (RRID:SCR_008871) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gma

Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure.

Proper citation: GMA (RRID:SCR_009212) Copy   

•   Source: SciCrunch Registry

http://www.readout.info

Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.

Proper citation: Neural Decoding Toolbox (RRID:SCR_009012) Copy   

•   Source: SciCrunch Registry

http://animaltracker.elte.hu/

A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.

Proper citation: AnimalTracker (RRID:SCR_014397) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.olympus-lifescience.com/en/software/cellsens/

Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.

Proper citation: Olympus cellSens Software (RRID:SCR_014551) Copy   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/free_services/relibase_free

Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions.

Proper citation: Relibase (RRID:SCR_014888) Copy   

•   Source: SciCrunch Registry

http://www2.chemie.uni-erlangen.de/software/cactvs/

Computational chemistry related-software used for the computation management, analysis and visualisation of chemical information of any defined type. This software uses a worldwide network of databases with property descriptions, computational modules, data analysis tools, visualization servers, data type handlers and I/O modules to increase the software�s capacity extensibility.

Proper citation: CACTVS System (RRID:SCR_014919) Copy   

•   Source: SciCrunch Registry

http://www.analog-electronics.eu/slicap/slicap.html

A software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits.

Proper citation: SLiCAP (RRID:SCR_014742) Copy   

•   Source: SciCrunch Registry

https://www.mirion.com/products/genie-2000-basic-spectroscopy-software

Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.

Proper citation: Genie 2000 Basic (RRID:SCR_021933) Copy   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Proper citation: ToppCluster (RRID:SCR_001503) Copy   

•   Source: SciCrunch Registry

https://github.com/QMICodeBase/TORTOISEV4

An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.

Proper citation: TORTOISE (RRID:SCR_001645) Copy   

•   Source: SciCrunch Registry

http://www.GeneWeaver.org

Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.

Proper citation: Gene Weaver (RRID:SCR_003009) Copy   

•   Source: SciCrunch Registry

http://seer.cancer.gov/resources/

Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.

Proper citation: SEER Datasets and Software (RRID:SCR_003293) Copy   

•   Source: SciCrunch Registry