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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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POLGUI - Matlab Polhemus Interface Resource Report Resource Website 1+ mentions |
POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) | POLGUI | software resource | An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows) | eeg, meg, electrocorticography, linux, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
BSD License | nlx_155915 | http://www.nitrc.org/projects/polgui | SCR_006752 | POLGUI - Matlab GUI for Polhemus Fastrak | 2026-09-12 12:56:45 | 5 | ||||||
|
RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html, https://bio.tools/ramigo | SCR_006922 | ramigo, RamiGO - AmiGO visualize R interface | 2026-09-12 12:56:47 | 12 | |||||
|
RazerS Resource Report Resource Website 10+ mentions |
RazerS (RRID:SCR_006889) | RazerS | software resource | A read mapping software program with adjustable sensitivity based on counting q-grams. RazerS 3 supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers? bit-vector algorithm for verification, memory saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular long reads with many errors. | next-generation sequencing, c++, openmp, linux, mac os x, windows |
is listed by: OMICtools has parent organization: Free University of Berlin; Berlin; Germany |
PMID:22923295 PMID:19592482 |
GNU General Public License | OMICS_00679 | SCR_006889 | 2026-09-12 12:56:47 | 13 | |||||||
|
Matlab Neuroshare Library Resource Report Resource Website |
Matlab Neuroshare Library (RRID:SCR_006957) | NeuroshareLibrary | software library, software resource, software toolkit | This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file. | console (text based), eeg, meg, electrocorticography, format conversion, japanese, linux, macos, matlab, microsoft, posix/unix-like, windows, neuroshare, data format, data sharing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ATR; Kyoto; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | GNU General Public License | nlx_155880 | http://www.nitrc.org/projects/nslib_v1_3_1 | SCR_006957 | Neuroshare Library | 2026-09-12 12:56:48 | 0 | |||||
|
NPTK Resource Report Resource Website |
NPTK (RRID:SCR_002496) | NPTK | data processing software, image analysis software, registration software, software application, software resource | Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI. | analyze, artifact removal, c++, image-to-image, intermodal, linux, macos, microsoft, magnetic resonance, nifti, nonlinear warp, posix/unix-like, registration, spatial transformation, warping, windows, windows xp, fmri, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155893 | SCR_002496 | 2026-09-12 12:55:41 | 0 | ||||||||
|
PaleoVu Resource Report Resource Website |
PaleoVu (RRID:SCR_002411) | PaleoVu | data processing software, data visualization software, software application, software resource | A complete browse and visualization tool for all types of paleoclimate and paleoecological data (Version 1.0 for Windows 3.1 and the Macintosh). Point and click to create queries, list site information, display or plot variables and data, or export the data for further processing and analysis. Note: PaleoVu is no longer maintained or supported. Data content is not being updated, and compatibility problems may exist with newer operating systems. PaleoVu is still suitable as a teaching tool, but our internet-based browsing tools are the most up to date source for paleoclimatic data. | browse, visualization, paleo, paleoclimatology, ecology, paleoclimate, climate, query, windows, macintosh, paleoecological |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
Free | SciRes_000130 | SCR_002411 | 2026-09-12 12:55:40 | 0 | ||||||||
|
flowBeads Resource Report Resource Website |
flowBeads (RRID:SCR_002440) | software resource | Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
uses: flowCore is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available | OMICS_05592 | SCR_002440 | flowBeads: Analysis of flow bead data | 2026-09-12 12:55:41 | 0 | ||||||||
|
flowCyBar Resource Report Resource Website 1+ mentions |
flowCyBar (RRID:SCR_002319) | software resource | A software package to analyze flow cytometric data using gate information to follow population / community dynamics. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_05597 | SCR_002319 | flowCyBar - Analyze flow cytometric data using gate information | 2026-09-12 12:55:39 | 7 | ||||||||
|
GLIRT Resource Report Resource Website |
GLIRT (RRID:SCR_002390) | GLIRT | data processing software, image analysis software, registration software, software application, software resource | Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously. | analyze, application, c++, image-to-image, intersubject, linux, microsoft, motion analysis, magnetic resonance, posix/unix-like, registration, software, spatial transformation, temporal transformation, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
Free | nlx_155763 | http://www.nitrc.org/projects/glirt | SCR_002390 | Groupwise and Longitudinal Image Registration Toolbox | 2026-09-12 12:55:40 | 0 | ||||||
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BRAINSFit Resource Report Resource Website 10+ mentions |
BRAINSFit (RRID:SCR_002340) | BRAINSFit | data processing software, image analysis software, registration software, software application, software resource | A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3 | affine warp, analyze, c++, console (text based), dicom, image-to-image, intermodal, intersubject, linear warp, macos, microsoft, magnetic resonance, nifti, os independent, posix/unix-like, registration, spatial transformation, warping, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155701 | http://www.nitrc.org/projects/multimodereg | SCR_002340 | 2026-09-12 12:55:39 | 20 | |||||||
|
MBASED Resource Report Resource Website 10+ mentions |
MBASED (RRID:SCR_002584) | software resource | Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection. | software package, unix/linux, mac os x, windows, r, gene expression, sequencing, transcription |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25315065 | Free, Available for download, Freely available | OMICS_05502 | http://www.bioconductor.org/packages/release/bioc/html/MBASED.html | SCR_002584 | Meta-analysis Based Allele-Specific Expression Detection, MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection | 2026-09-12 12:55:43 | 17 | ||||||
|
WFU Biological Parametric Mapping Toolbox Resource Report Resource Website 1+ mentions |
WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) | WFU_BPM, WFU BPM | data processing software, image analysis software, software application, software resource, software toolkit | Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher | analyze, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, statistical operation, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Wake Forest School of Medicine; North Carolina; USA |
Human Brain Project ; NIBIB 1R01EB004673 |
PMID:17070709 | Free, Available for download, Freely available | nlx_156016 | http://www.nitrc.org/projects/wfu_bpm | SCR_002613 | BPM - Integrated Tool for Biological Parametric Mapping, WFU Biological Parametric Mapping, BPM toolbox, BPM | 2026-09-12 12:55:43 | 4 | ||||
|
Vaa3D Resource Report Resource Website 100+ mentions |
Vaa3D (RRID:SCR_002609) | Vaa3D, Vaa3D-Neuron | data management software, data processing software, data visualization software, image analysis software, software application, software resource, software toolkit | A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools. | reusable library, atlas application, c, c++, cygwin, fiber tracking, gnome, image display, kde, linux, macos, microsoft, magnetic resonance, neuronal characterization, development environment, position, posix/unix-like, quantification, registration, rendering, resampling, segmentation, shape analysis, spatial transformation, surface analysis, tractography, visualization, volumetric analysis, warping, win32 (ms windows), windows, windows 95/98/2000, windows nt/2000, windows vista, windows xp, 3d neuron reconstruction, 3d, neuron, reconstruction, microscopy |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Insight Segmentation and Registration Toolkit has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | Free, Available for download, Freely available | nlx_156012 | http://www.nitrc.org/projects/v3d | SCR_002609 | V3D, Vaa3D: A Swiss army knife for bioimage visualization & analysis, V3D-Neuron, Vaa3D: A Swiss army knife for bioimage visualization and analysis, 3D Visualization-Assisted Analysis, Vaa3D and Vaa3D-Neuron | 2026-09-12 12:55:43 | 166 | ||||
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TurtleSeg Resource Report Resource Website 1+ mentions |
TurtleSeg (RRID:SCR_002605) | TurtleSeg | data processing software, image analysis software, segmentation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process. | analyze, c++, computed tomography, dicom, intensity contour, microsoft, minc, magnetic resonance, nifti, segmentation, win32 (ms windows), windows, windows nt/2000, windows vista, windows xp | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156008 | http://www.nitrc.org/projects/turtleseg | SCR_002605 | TurtleSeg - Interactive 3D Image Segmentation Software | 2026-09-12 12:55:43 | 6 | ||||||
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DSS Resource Report Resource Website 1+ mentions |
DSS (RRID:SCR_002754) | software library, software resource, software toolkit | Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. | standalone software, unix/linux, mac os x, windows, r, differential expression, rna-seq, chip-seq, dna methylation, differential expression, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24561809 | Free, Freely available, Available for download | OMICS_03273 | SCR_002754 | Dispersion Shrinakge for Sequencing data, DSS - Dispersion shrinakge for sequencing data | 2026-09-12 12:55:46 | 9 | |||||||
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rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser, https://bio.tools/rbiopaxparser | SCR_002744 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-09-12 12:55:45 | 4 | ||||||
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aCGH.Spline Resource Report Resource Website |
aCGH.Spline (RRID:SCR_002927) | software resource | An R package for array comparative genomic hybridization (aCGH) dye bias normalization. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21357574 | Free, Available for download, Freely available | OMICS_02607 | http://cran.r-project.org/web/packages/aCGH.Spline/ | SCR_002927 | 2026-09-12 12:55:48 | 0 | |||||||
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Basic4Cseq Resource Report Resource Website 1+ mentions |
Basic4Cseq (RRID:SCR_002836) | software resource | An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. | software package, unix/linux, mac os x, windows, r, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25078398 | Free, Freely available, Available for download | OMICS_05202 | SCR_002836 | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data | 2026-09-12 12:55:47 | 6 | |||||||
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mzR Resource Report Resource Website 1+ mentions |
mzR (RRID:SCR_002856) | software resource | Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | standalone software, mac os x, unix/linux, windows, r, data import, infrastructure, mass spectrometry, metabolomics, proteomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02654 | SCR_002856 | mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files | 2026-09-12 12:55:47 | 1 | ||||||||
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BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-09-12 12:55:47 | 0 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
