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http://imaging.indyrad.iupui.edu/projects/SPHARM/

A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics.

Proper citation: SPHARM-MAT (RRID:SCR_002545) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/brain.org.au/ctp/

Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cortex (RRID:SCR_002467) Copy   

•   Source: SciCrunch Registry

http://www.genetics.emory.edu/labs/epstein/software/chaplin/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software)

Proper citation: CHAPLIN (RRID:SCR_000833) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/crimap.shtml

Software application for constructing multilocus linkage map (entry from Genetic Analysis Software)

Proper citation: CRIMAP (RRID:SCR_000834) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.ic.ac.uk/eqtlexplorer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software)

Proper citation: EQTL EXPLORER (RRID:SCR_001123) Copy   

•   Source: SciCrunch Registry

http://www.egi.com/research-division-geodesic-system-components/eeg-software

A complete software package for working with electroencephalography (EEG) and event-related potential (ERP) data. You can acquire, review, analyze, and now ?see? your participant with synchronized video. Net Station also offers specialized tools and workflow options for both clinical and research applications, allows you to save different combinations of view settings (called workspaces) and helps with your reporting requirements by letting you set up and print custom cover pages. For more specialized work, Net Station also provides an optional electrical source estimation module (GeoSource) and an optional sensor location digitizer (Geodesic Photogrammetry System).

Proper citation: Net Station EEG Software (RRID:SCR_002453) Copy   

•   Source: SciCrunch Registry

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

An open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the user's manual segmentation using the image data and manual segmentation provided by the user. The motivation of this project is to bridge the gap between the segmentation tool developer and the tool users such that the existing segmentation tools can more effectively serve the community. More and more automatic segmentation tools are publicly available to today's researchers. However, when applied by their end-users, these segmentation tools usually can not achieve the performance that the tool developer reported. Discrepancies between the tool developer and its users in manual segmentation protocols and imaging modalities are the main reasons for such inconsistency.

Proper citation: Automatic Segmentation Tool Adapter (RRID:SCR_002481) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/targetgene/

MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7

Proper citation: TARGETgene (RRID:SCR_001392) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/beagle/beagle.html

Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

Proper citation: BEAGLE (RRID:SCR_001789) Copy   

•   Source: SciCrunch Registry

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

Software tool to detect physiologic signals from the data itself as well as an adaptive physiologic noise removal tool (Impulse Response Function or IRF-RETROICOR) that zooms in on noise with only 6 regressors, getting all the noise that 5th order RETROICOR gets. These tools will allow you to correct your data for physiologic noise with what you currently have. These signals are equivalent to a parallel monitored pulse signal and a respiratory chest-bellows signal. Do you have 3D+time EPI data (BOLD or perfusion) but no usable physio signals for pulse and respiration? Are you concerned about the effect of physio noise on your data but don't know what to do but regress data-derived signals that mix unknown functional signal with possible physio noise signal? Are you concerned about the number of regressors you're incorporating once you add 5th order RETROICOR (20 more regressors!)? This is for you.

Proper citation: PESTICA fMRI Physio Detection/Correction (RRID:SCR_002513) Copy   

•   Source: SciCrunch Registry

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

Standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties. Use the MEDIAWIKI entry in the menu on the left for more information about the CIFTI file formats. Access the CIFTI discussion forum using the Forums entry in the menu on the left. Subscribe to the discussion forum and you will be informed about issues involving the CIFTI file formats via email.

Proper citation: CIFTI Connectivity File Format (RRID:SCR_000852) Copy   

•   Source: SciCrunch Registry

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

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

https://www.apbenson.com/cyrillic-downloads

Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.

Proper citation: CYRILLIC (RRID:SCR_001823) Copy   

•   Source: SciCrunch Registry

http://openmeeg.gforge.inria.fr

A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy.

Proper citation: OpenMEEG (RRID:SCR_002510) 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.crl.med.harvard.edu/software/STAPLE/index.php

An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: STAPLE (RRID:SCR_002590) 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://nipy.org/nipype/

A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

Proper citation: Nipype (RRID:SCR_002502) 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.medtronic.com/

Medical technology company that develops and manufactures devices and therapies to treat more than 30 chronic diseases, including heart failure, Parkinson's disease, urinary incontinence, Down syndrome, obesity, chronic pain, spinal disorders, and diabetes. A Commercial healthcare organization for both patients and healthcare professionals. For professionals, it provides products, therapy and procedure solutions, and services.

Proper citation: Medtronic (RRID:SCR_003988) Copy   

•   Source: SciCrunch Registry