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https://github.com/jyeatman/AFQ
A framework for generating Tract Profiles of tissue properties for major fiber tracts in healthy and diseased brains. Online documentation can be found at: https://github.com/yeatmanlab/AFQ/wiki. AFQ has been tested for MATLAB r2009b through MATLAB r2014b. It requires functions from the MATLAB stats toolbox, vistasoft and SPM.
Proper citation: AFQ: Automated Fiber Quatification (RRID:SCR_014546) Copy
https://github.com/NCBI-Hackathons/PhenVar
Software tool used to generate a list of PubMed IDs to query and generate associations between publications. It utilizes a local SQLite cache in a configurable location to keep a local copy of relevant SRIDs, PMIDs, and the Abstract sections for the PMIDs.
Proper citation: PhenVar (RRID:SCR_015515) Copy
A biomaterial supply resource which collects and disseminates human heart tissue. Samples include both failing and non-failing hearts, RNA/DNA analysis, tissue staining and immunofluorescence samples.The tissue that has been flash frozen and stored at -80˚C is acquired from distinct regions of the heart such as the LV free wall, septum, and valve leaflets. Individual sample sizes are typically 100-300mg for flash frozen tissues. The DHHR also serves as a resource for assay development, target identification, and sponsored research, capable of isolating cardiomyocytes from hearts and using them for in-vitro assays such as calcium handling, enzyme activity, signalling pathways and other biochemical research activities
Proper citation: Duke Human Heart Repository (RRID:SCR_013980) Copy
http://brainhealthregistry.org/
A website aimed at recruiting and assessing subjects for all types of neuroscience studies with the internet. The hope is to accelerate various types of observational studies and clinical trials, and also reduce costs. They are interested in having people, including healthy subjects of all ages, join the registry. Joining only takes a few minutes. The web-based project is designed to speed up cures for Alzheimer's, Parkinson's and other brain disorders. It uses online questionnaires and online neuropsychological tests (which are very much like online brain games).
Proper citation: Brain Health Registry (RRID:SCR_010230) Copy
https://imdevsoftware.wordpress.com/imdev/
A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.
Proper citation: imDEV (RRID:SCR_014674) Copy
http://www.avisoft.com/soundanalysis.htm
Sound analysis software used to process and analyze animal acoustic communications. Its features include digital filtering, real-time spectrogram display, and advanced metadata management. Avisoft SASLabPro is designed to accommodate large numbers of sound files and includes organizational features, including labeling options for single point data and time section labels.
Proper citation: Avisoft SASLabPro (RRID:SCR_014438) Copy
A software repository which provides open source software and technology for visualization, computer vision, medical imaging, data publishing, and quality software process solutions. Kitware also provides services such as creating customized applications for clients, porting their open-source tools to specialized computing platforms, and supporting their open-source software tools with documentation, professional consulting services, and software training.
Proper citation: Kitware (RRID:SCR_013989) Copy
https://europepmc.org/annotations
Text mining tool from Europe PMC that allows biological terms or concepts to be highlighted for readers on full text articles. These terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. However, it is up to the reader to control which selection of highlighted concepts they see. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model and stored in a triple store via the EMBL-EBI RDF Platform. As a reader views an article in a web browser, any annotations in the triple store associated with the article are made available in a menu alongside the article.
Proper citation: SciLite (RRID:SCR_015015) Copy
http://xoonips.sourceforge.jp/
Neuroinformatics (NI) is a new discipline that challenges the understanding of the structure and mechanism of the brain by combining neuroscience and information technology. The global collaborations in this field have been actively started with the support of the International Neuroinformatics Coordinating Facility (INCF) launched in November 2005. The Laboratory for Neuroinformatics at RIKEN Brain Science Institute (BSI) is involved in developing various cutting-edge technologies related to NI such as XooNIps. XooNIps succeeded the concept and basic feature of the vision science platform; Visiome, constructed by the NRV (i.e., Neuroinformatics Research in Vision) Project and has been developed based on a content management system (CMS); XOOPS, as infrastructure for NI databases to share different types of data on the Internet. :XooNIps has three features: :The first is the flexibility of developing databases. CMS-based XooNIps makes it easy to change the design or to extend the functions of databases by combining the different modules available on XOOPS. Therefore, even those who are not expert in computer system can develop their database on XooNIps. :The second is the diversity and extensibility of the data which can be handled by XooNIps. In order to handle different types of actual data, it provides not only the various data forms per se, but also the extension method to handle a new data form, which enables to deal easily with even a non-standardized data form. :The third is the facility to distribute metadata. XooNIps implements OAI-PMH (i.e., Open Archive Initiative-Protocol for Metadata Harvesting) which is one of the standard protocols to distribute metadata. This enables to collect information on other databases which are developed on XooNIps or to coordinate databases by exchanging metadata with other databases which implement OAI-PMH than those on XooNIps. :Since April 2007, Neuroinformatics Japan Center (NIJC) at RIKEN BSI takes charge of extending and maintaining XooNIps, and is committed to manage the documentation hereafter. :NIJC, as a national node of INCF, is developing and operating various NI platforms in neuroscience based on XooNIps to establish and facilitate NI research in Japan. XooNIps is also being applied to databases or organizational repositories in several institutions and universities, and laboratory groupware in various fields. We hope XooNIps will be of universal use in and out of Japan. :database; binary executable; software development tool; metadata; data set; :
Proper citation: XooNIps - Neuroinformatics Base Platform System (RRID:SCR_013590) Copy
https://github.com/im3sanger/dndscv
Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies.
Proper citation: dNdScv (RRID:SCR_023123) Copy
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
https://github.com/AlexandrovLab/SigProfilerExtractor/
Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample.
Proper citation: SigProfilerExtractor (RRID:SCR_023121) Copy
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
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
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
https://bioconductor.org/packages/DEP/
Software R package provides integrated analysis workflow for analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment.
Proper citation: Differential Enrichment analysis of Proteomics data (RRID:SCR_023090) Copy
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
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
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
A group which aims to create open standards for metabolomics data shsaring and analysis.
Proper citation: Coordination of Standards in Metabolomics (RRID:SCR_014662) Copy
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