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http://www.cytobank.org/index.html

A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.

Proper citation: Cytobank (RRID:SCR_014043) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/ruby-nifti/

A library for handling NIfTI data in the Ruby programming language. Ruby NIfTI supports basic read and write access to NIfTI files, including basic and extended header information and image information. It doesn't attempt to touch the image data but it does provide access to qform and sform orientation matrices. It also provides a nice interface to get at NIfTI info from within Ruby.

Proper citation: Ruby NIfTI (RRID:SCR_014164) Copy   

•   Source: SciCrunch Registry
  

http://www.sci.utah.edu/cibc-research/highlights/24-research-highlights/cibc-highlights/221-scirun-biopse.html

A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems.

Proper citation: BioPSE (RRID:SCR_014044) Copy   

•   Source: SciCrunch Registry
  

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

A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard.

Proper citation: SCORE (RRID:SCR_014165) Copy   

•   Source: SciCrunch Registry
  

http://www.statcrunch.com

A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available.

Proper citation: StatCrunch (RRID:SCR_013992) Copy   

•   Source: SciCrunch Registry
  

https://www.wakari.io

A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as "bundles" with other users, who can edit and download them.

Proper citation: Wakari (RRID:SCR_013995) Copy   

•   Source: SciCrunch Registry
  

https://muhc.ca

A public health center and research institution affiliated with McGill University.

Proper citation: McGill University Health Centre; Quebec; Canada (RRID:SCR_014048) Copy   

•   Source: SciCrunch Registry
  

http://www.bio-rad.com/en-us/product/quantity-one-1-d-analysis-software

Software used for Bio-Rad imaging systems to acquire, quantitate, and analyze a variety of data. The software allows automatic configuration of imaging systems with appropriate filters, lasers, LEDs, and other illumination sources. It also contains tools for automated analysis of tests and assays such as 1-D electrophoretic gels, western blots, and colony counts.

Proper citation: Quantity One 1-D Analysis Software (RRID:SCR_014280) Copy   

•   Source: SciCrunch Registry
  

https://www.ebi.ac.uk/chembl/

Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.

Proper citation: ChEMBL (RRID:SCR_014042) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/pca-scalar-mesh

An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class, where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class.

Proper citation: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data (RRID:SCR_014163) Copy   

•   Source: SciCrunch Registry
  

http://downloads.thermofisher.com/Instrument_Software/qPCR/Step-1/SOP23_Release%20Notes_4482516.pdf

A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data.

Proper citation: StepOne Software (RRID:SCR_014281) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/cmind_py_2014/

A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project.

Proper citation: CMIND PY (RRID:SCR_014097) Copy   

•   Source: SciCrunch Registry
  

http://www.scilifelab.se

A Swedish national center of research for molecular biosciences with a focus on health and environmental research. Researchers from Sweden can use both the technology and the expertise provided by SciLifeLab. Swedish researchers typically pay only for reagents and other consumables. Users from commercial companies pay the actual costs of the analyses performed. SciLifeLab also provides educational courses, seminars, and programs for PhD students, postdocs, investigators and other employees within all Swedish universities.

Proper citation: SciLifeLab (RRID:SCR_014078) Copy   

•   Source: SciCrunch Registry
  

http://www.creative-peptides.com/Peptide-synthesis.html

A reagent manufacturer which provides custom peptide APIs and custom peptide synthesis services. These products and services include high throughput peptide library/array synthesis, high quality bulk API peptides, bioactive catalog peptides, and cosmetic peptides.

Proper citation: Peptide Synthesis (RRID:SCR_014070) Copy   

•   Source: SciCrunch Registry
  

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

A large scale functional connectivity data mining software package which enables large-scale seed-based analysis and brain-behavior analysis. It can examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables.

Proper citation: Advanced Connectivity Analysis (ACA) (RRID:SCR_014195) Copy   

•   Source: SciCrunch Registry
  

http://dbm.neuro.uni-jena.de/vbm/

A collection of extensions to the segmentation algorithm of SPM2, SPM5, and SPM8 to provide voxel-based morphometry. The toolboxes are named according to the SPM version. The software is available to the scientific community under the terms of the GNU General Public License. VBM subpages can be accessed from the VBM website.

Proper citation: VBM toolbox (RRID:SCR_014196) Copy   

•   Source: SciCrunch Registry
  

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 11, 2015. A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG).

Proper citation: Biomag Discussion Group on Yahoo (RRID:SCR_014089) Copy   

•   Source: SciCrunch Registry
  

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

A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures.

Proper citation: APERTURE (RRID:SCR_014082) Copy   

•   Source: SciCrunch Registry
  

http://www.photonics.com/Product.aspx?PRID=47380

Image processing software used to modify and clarify sample images for FluoView FV1000 range of confocal laser scanning microscopes and Fluoview FV1000MPE multiphoton excitation systems. The software incorporates high-dynamic-range imaging, minimized signal-to-noise ratios, partial stitching with multiarea time-lapse imaging, and channel unmixing. The software also allows users to select specific areas of the whole sample, which can stitched together.

Proper citation: FluoView FV10-ASW software (RRID:SCR_014215) Copy   

•   Source: SciCrunch Registry
  

https://www.phenix-online.org/documentation/reference/phaser.html

Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods.

Proper citation: Phaser (RRID:SCR_014219) Copy   

•   Source: SciCrunch Registry