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http://clip.med.yale.edu/presto/

Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.

Proper citation: pRESTO (RRID:SCR_001782) Copy   

•   Source: SciCrunch Registry

http://neuro.debian.net/pkgs/cmtk.html

A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.

Proper citation: Computational Morphometry Toolkit (RRID:SCR_002234) Copy   

•   Source: SciCrunch Registry

http://www.math.hkbu.edu.hk/~mng/CLUSTAG/CLUSTAG.html

Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment.

Proper citation: CLUSTAG (RRID:SCR_001816) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/

An open bioinformatis software repository with no tie to any organization or institution. Contact them to host your software.

Proper citation: OpenBioinformatics.org (RRID:SCR_002229) Copy   

•   Source: SciCrunch Registry

http://dataferrett.census.gov

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2025. A data analysis and extraction tool from the US Census Bureaus with recoding capabilities to customize federal, state, and local data to suit your requirements. DataFerret works with the DataWeb, a network of online data libraries and an infrastructure for intelligent browsing. TheDataweb provides easy access to data from disparate locations across the internet using DataFerrett as its interface. It brings together demographic, economic, environmental, health, and other datasets that are usually separated by geography and/or organization.Using DataFerrett, you can develop an unlimited array of customized spreadsheets that are as versatile and complex as your usage demands. For a listing/description of datasets available using the DataFerrett refer to the Datasets Available tab. DataFerrett helps you locate and retrieve the data you need across the Internet to your desktop or system, regardless of where the data resides. You can develop and customize tables and select the results to create a graph or map for a visual depiction of your data. You can also save your data in the databasket and save the table you have created for reuse. The DataFerrett tool can use a java applet through an internet browser or be installed as an application on your desktop. The DataFerrett Applet requires you to have popup windows enabled in your browser for this website to function properly.

Proper citation: TheDataWeb and DataFerrett (RRID:SCR_003197) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/

An integrated set of tools for measuring cognitive, emotional, motor and sensory function. These tools are being validated for use in diverse cultures, ethnic and geographic groups, ages (3-85 years) and study types. The toolbox is expected to provide a more complete picture of neurological and behavioral health in large-scale longitudinal studies, epidemiological studies, and clinical trials; and to facilitate cross-study comparisons. Moreover, the toolbox will: * be minimally burdensome to subjects and investigators, * utilize state-of-the art psychometric approaches and technology, including computer-assisted evaluation, and * be dynamic and adaptable to changes in measurement and technology. * be available in English and Spanish Many clinical studies collect data on aspects of neurological and behavioral function. However, the neurological and behavioral tests currently available to researchers lack uniformity and often require specialized training to administer. These limitations make it difficult to compile data across the full range of normal neurological function, and to compare data across studies. The toolbox is royalty-free and is expected to be available online by summer 2012.

Proper citation: NIH Toolbox - Assessment of Neurological and Behavioral Function (RRID:SCR_002423) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/WhatAndWhy/Motor/Locomotion/Pages/NIH-Toolbox-4--Meter-Walk-Gait-Speed-Test.aspx

Assessment test to measure gait speed where participants are asked to walk a short distance (4 meters) at their usual pace. Participants complete one practice and then two timed trials. Raw scores are recorded as the time in seconds required to walk 4 meters on each of the two trials, with the better trial used for scoring. The 4-Meter Walk Gait Speed Test is adapted from the 4-meter walk test in the Short Physical Performance Battery. The test takes approximately 3 minutes to administer (including instructions and practice). This test is recommended for ages 7-85.

Proper citation: NIH Toolbox 4-Meter Walk Gait Speed Test (RRID:SCR_003632) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/WhatAndWhy/Motor/Endurance/Pages/NIH-Toolbox-2-Minute-Walk-Endurance-Test.aspx

Assessment test that measures sub-maximal cardiovascular endurance by recording the distance that the participant is able to walk on a 50-foot (out and back) course in 2 minutes. The participant's raw score is the distance in feet and inches walked in 2 minutes. The test is adapted from the American Thoracic Society's 6-Minute Walk Test Protocol. The test overall takes approximately 4 minutes to administer (with instructions and practice). This test is recommended for ages 3-85.

Proper citation: NIH Toolbox 2-Minute Walk Endurance Test (RRID:SCR_003631) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/VennDiagram/

Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Proper citation: VennDiagram (RRID:SCR_002414) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/WhatAndWhy/Motor/Balance/Pages/Balance.aspx

A measure to assess static standing balance that involves the participant assuming and maintaining up to 5 poses for 50 seconds each. The sequence of poses is: eyes open on a solid surface, eyes closed on solid surface, eyes open on foam surface, eyes closed on foam surface, eyes open in tandem stance. Detailed stopping rules are in place to ensure participant safety with these progressively demanding poses. Postural sway is recorded for each pose using an accelerometer that the participant wears at waist level. This test takes approximately 7 minutes to administer and is recommended for ages 3-85.

Proper citation: NIH Toolbox Standing Balance Test (RRID:SCR_003628) Copy   

•   Source: SciCrunch Registry

https://neuro-jena.github.io/software.html#tom

Software toolbox for creating customized pediatric templates. It provides reference data based on imaging data from the NIH study of normal brain development. Using the general linear model, they statistically isolate the influence of external variables of interest on brain structure, allowing us to generate high-quality matched templates for any given group of subjects. The toolbox offers two options: # to create pediatric templates (T1) and tissue maps (GM, WM, and CSF) based on the objective 1 NIH data (n = 404), in the age range of 5-18 years, or # to assess a new reference population with regard to your variables of interest. Of note, this approach is generally applicable and in no way restricted to analyzing pediatric imaging data: for example, if you aim at investigating the effects of aging in elderly subjects, the toolbox will also allow you to create more appropriate reference (if your group is large enough to isolate such effects).

Proper citation: Template-O-Matic Toolbox (RRID:SCR_003220) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/muma/

Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).

Proper citation: MUMA (RRID:SCR_002412) Copy   

•   Source: SciCrunch Registry

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

So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171).

Proper citation: RFT FDR (RRID:SCR_002533) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/WhatAndWhy/Cognition/Language/Pages/NIH-Toolbox-Oral-Reading-Recognition-Test.aspx

Assessment test that measures the ability of patients to identify words and letters. The participant is asked to read and pronounce letters and words as accurately as possible. The test administrator scores them as right or wrong. For the youngest children, the initial items require them to identify letters (as opposed to symbols) and to identify a specific letter in an array of 4 symbols. The test is given in a computerized adaptive format and requires approximately 3 minutes. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested. Separate but parallel reading tests have been developed in English and in Spanish.

Proper citation: NIH Toolbox Oral Reading Recognition Test (RRID:SCR_003622) Copy   

•   Source: SciCrunch Registry

http://www.lifesciences.sourcebioscience.com/welcome-to-source-bioscience-lifesciences.aspx

Source BioScience LifeSciences are European leaders in DNA sequencing, genomic services, bioinformatic analyses and offers a comprehensive portfolio of genomic reagents and antibodies. Source BioScience LifeScience is a CPA, GLP/GCP accredited and Illumina NGS CSPro certified genomic service provider and distributes a comprehensive range of biological products to companies and institutions worldwide. Source BioScience is proud to announce that Source BioScience imaGenes has joined it's LifeSciences group. This will enable us to bring our customers one unified website with our complete range of Products, Clones and Services. We have merged our clone libraries together so that can now offer you over 20 million clones! Add to this our excellent sequencing service and our range of over 100,000 antibodies and Source BioScience LifeSciences is your ideal outsourcing partner.

Proper citation: Source BioScience LifeSciences (RRID:SCR_003344) Copy   

•   Source: SciCrunch Registry

http://www.mountsinai.on.ca/allograft/

Mount Sinai Allograft Technologies, a department of Mount Sinai Hospital formerly known as the The Rubinoff Bone Bank, has been a leader in advanced tissue innovations since 1972. We are committed to providing the highest quality bone and tissue allograft products as well as continued innovation in the development of allograft implants for transplantation. We are dedicated to meeting all surgical needs and to exceed all client expectations. We work closely with the Trillium Gift of Life Network to promote their mission of increasing donor awareness and to ensure that the wishes of Ontario donor families' are carried out with the utmost care and respect. Our allograft implants are 100% Ontario produced, human allograft tissues. To produce the safest and highest quality Canadian produced allograft implants, Mount Sinai Allograft Technologies leverages the expertise of a variety of medical experts, state-of-the art laboratory testing, proven bio-processing techniques, validated irradiation methods and preferred packaging systems.

Proper citation: Mount Sinai Allograft Technologies (RRID:SCR_003586) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nirx2nirs/

A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge.

Proper citation: NIRx2nirs: A NIRx to .nirs data converter (RRID:SCR_002492) Copy   

•   Source: SciCrunch Registry

https://omictools.com/prolinks-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage.

Proper citation: ProLinks Database of Functional Linkages (RRID:SCR_003185) Copy   

•   Source: SciCrunch Registry

http://www.mbfbioscience.com/stereo-investigator

Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology.

Proper citation: MBF BioScience: Stereo Investigator (RRID:SCR_002526) Copy   

•   Source: SciCrunch Registry

http://www.preger.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods.

Proper citation: Primate Embryo Gene Expression Resource (RRID:SCR_002765) Copy   

•   Source: SciCrunch Registry