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http://omicslab.genetics.ac.cn/ISRNA/

An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ISRNA (RRID:SCR_009565) Copy   

•   Source: SciCrunch Registry

http://www.nordicneurolab.com

From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike.

Proper citation: NordicNeuroLab (RRID:SCR_009632) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/masimatlab/

This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling.

Proper citation: MASIMatlab (RRID:SCR_009506) Copy   

•   Source: SciCrunch Registry

http://www.smivision.com/en/gaze-and-eye-tracking-systems/products/iview-x-mri-meg.html

A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output

Proper citation: iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/masi-fusion/

Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided.

Proper citation: MASI Label Fusion (RRID:SCR_009505) Copy   

•   Source: SciCrunch Registry

http://www.rogue-research.com

Neuronavigation system for use in human cognitive neuroscience (TMS, EEG, NIRS) and for non-human neurosurgical applications.

Proper citation: Brainsight (RRID:SCR_009539) Copy   

•   Source: SciCrunch Registry

http://www.labmedmolge.unisa.it/inglese/research/imir

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.

Proper citation: iMir (RRID:SCR_009496) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

http://www.vpixx.com/products/visual-stimulators/datapixx.html

Supplies a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor, the DATAPixx includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision.

Proper citation: DATAPixx (RRID:SCR_009648) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/rbpm/

To enable widespread application of the Biological parametric mapping (BPM) approach, they introduce robust regression and non-parametric regression in the neuroimaging context of application of the general linear model. Biological parametric mapping (BPM) has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects.

Proper citation: Robust Biological Parametric Mapping (RRID:SCR_009642) Copy   

•   Source: SciCrunch Registry

http://www.ohsu.edu/xd/

As the state''s only health and research university, OHSU brings together patient care, research, education of the next generation of health care providers and scientists and community service to improve the health and well-being of all Oregonians.

Proper citation: Oregon Health and Science University; Oregon; USA (RRID:SCR_009665) Copy   

•   Source: SciCrunch Registry

http://www.commerce.gov/

Executive department of the federal government concerned with promoting economic growth. Among its tasks are gathering economic and demographic data for business and government decision-making, and helping to set industrial standards.

Proper citation: U.S. Department of Commerce (RRID:SCR_009859) Copy   

•   Source: SciCrunch Registry

http://www.usgs.gov/

Scientific agency of the United States government. The scientists of the USGS study the landscape of the United States, its natural resources, and the natural hazards that threaten it. The organization's work spans the disciplines of biology, geography, geology, and hydrology.

Proper citation: U.S. Geological Survey (RRID:SCR_010168) Copy   

•   Source: SciCrunch Registry

http://www.sdsu.edu/

Public research university in San Diego, California. Founded in 1897 as San Diego Normal School, it is the third-oldest university in the 23-member California State University system.

Proper citation: San Diego State University; California; USA (RRID:SCR_009874) Copy   

•   Source: SciCrunch Registry

http://dna.engr.uconn.edu/?page_id=105

Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.

Proper citation: IsoEM (RRID:SCR_009993) Copy   

•   Source: SciCrunch Registry

http://www.york.ac.uk/crd/

A research department of the University of York provides research-based information about the effects of health and social care interventions via their databases. The institute undertakes systematic reviews evaluating research evidence on health and public health questions of national and international importance.

Proper citation: Centre for Reviews and Dissemination (RRID:SCR_010267) Copy   

•   Source: SciCrunch Registry

http://www.sbg.bio.ic.ac.uk/phyre2

A structure prediction system to reliably detect remote homologies.

Proper citation: Phyre (RRID:SCR_010270) Copy   

•   Source: SciCrunch Registry

http://www.biobase-international.com

THIS RESOURCE IS OUT OF SERVICE, documented on February 1st,2022. BIOBASE offers academic and non-profit organizations free access to TRANSFAC?? non-professional version with much reduced functionality and content compared to our professional database.

Proper citation: BIOBASE Corporation (RRID:SCR_010271) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bitseq/

A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.

Proper citation: BitSeq (RRID:SCR_009904) Copy   

•   Source: SciCrunch Registry

http://www.dol.gov/

Fosters, promotes, and develops the welfare of the wage earners, job seekers, and retirees of the United States; improves working conditions; advances opportunities for profitable employment; and assures work-related benefits and rights.

Proper citation: U.S. Department of Labor (RRID:SCR_010157) Copy   

•   Source: SciCrunch Registry