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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | Meta-analysis Based Allele-Specific Expression Detection, MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection | 2026-11-07 11:54:53 | 17 | ||||||
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pymzML Resource Report Resource Website 10+ mentions |
pymzML (RRID:SCR_002500) | software resource | Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: mzML has parent organization: University of Munster; North Rhine-Westphalia; Germany |
PMID:22302572 | Free, Available for download, Freely available | biotools:pymzml, OMICS_03355 | https://bio.tools/pymzml | SCR_002500 | SciCrunch Registry | 2026-11-07 11:54:51 | 18 | |||||||
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ESTHER Resource Report Resource Website 100+ mentions |
ESTHER (RRID:SCR_002621) | ESTHER | data or information resource, database | Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | alpha hydrolase, beta hydrolase, cholinesterase, protein, protein superfamily, blast, gene, protein binding, protein-protein interaction, nucleotide, nucleotide sequence, enzyme, genetics, genome, genomics, mutation, disease, gene expression, peptide, chromosome |
is listed by: re3data.org is related to: UniProtKB is related to: AceDB has parent organization: INRA - French National Institute for Agricultural Research; Paris; France |
PMID:23193256 | Free, Available for download, Freely available | nif-0000-30526, SCR_008479, nif-0000-02817, r3d100010542 | https://doi.org/10.17616/R33K77 | SCR_002621 | SciCrunch Registry | ESTerases and alpha/beta-Hydrolase Enzymes and Relatives, ESTHER Database, ESTerases and alpha / beta-hydrolase Enzymes and Relatives | 2026-11-07 11:54:55 | 134 | |||||
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BioStar Resource Report Resource Website 50+ mentions |
BioStar (RRID:SCR_002580) | Biostar | community building portal, data or information resource, discussion, forum, narrative resource, portal | A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply. | bioinformatics, computational genomics, biological data analysis, data analysis, forum, question, answer |
is listed by: OMICtools is related to: NeuroStars |
NIH ; Luma Education ; NHGRI 5R25HG006243-02 |
PMID:22046109 | Free, Freely available | OMICS_01706, nlx_155982 | SCR_002580 | SciCrunch Registry | biostars.org | 2026-11-07 11:54:57 | 88 | |||||
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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 | SciCrunch Registry | BPM - Integrated Tool for Biological Parametric Mapping, WFU Biological Parametric Mapping, BPM toolbox, BPM | 2026-11-07 11:54:43 | 4 | ||||
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discoSnp Resource Report Resource Website 1+ mentions |
discoSnp (RRID:SCR_002612) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS). | single nucleotide polymorphism, snp discovery, discover snp, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
SOFIPROTEOL under the FASO project PEAPOL ; INRIA ANR-12-BS02-0008 |
PMID:25404127 | Free, Freely available | biotools:discosnp, OMICS_00267 | https://bio.tools/discosnp, https://sources.debian.org/src/discosnp/ | SCR_002612 | SciCrunch Registry | DiscoSnp++, discovering Single Nucleotide Polymorphism, discovering Single Nucleotide Polymorphism (discoSNP) | 2026-11-07 11:54:57 | 9 | |||||
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Etherpad Resource Report Resource Website 1+ mentions |
Etherpad (RRID:SCR_002611) | authoring tool, collaboration tool, software application, software resource, web application | Web application for real-time collaborative editing. It provides customizable options, a documented API and the ability to convert to various data exchange formats. | online word processor, collaborative application, writing tool | is listed by: FORCE11 | Free, Available for download, Freely available | nlx_156044 | SCR_002611 | SciCrunch Registry | 2026-11-07 11:54:42 | 5 | |||||||||
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University of Auckland; Auckland; New Zealand Resource Report Resource Website 1+ mentions |
University of Auckland; Auckland; New Zealand (RRID:SCR_002615) | university | Public university in New Zealand that offers degrees in areas such as the arts, business, education, medical and health science, and law. | public university system, new zealand, degree program |
is related to: University of Auckland Biomedical Imaging Research Unit Molecular Devices ImageXpress Micro XLS is parent organization of: CellML is parent organization of: BEAST2 is parent organization of: ApiNATOMY is parent organization of: University of Auckland Cytometry Core Facility |
Free | nlx_28115, Crossref Funder ID 501100001537, Wikidata Q492467, GRID grid.9654.e, ISNI 0000 0004 0372 3343 | https://ror.org/03b94tp07 | SCR_002615 | SciCrunch Registry | 2026-11-07 11:54:54 | 2 | ||||||||
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peak nii Resource Report Resource Website 1+ mentions |
peak nii (RRID:SCR_002572) | peak_nii | data processing software, image processing software, software application, software resource, software toolkit | Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command. | magnetic resonance, pet, spect | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Personal License | nlx_155975 | SCR_002572 | SciCrunch Registry | peak_nii: Statistical image clustering peak detection and data extraction, peak nii | 2026-11-07 11:54:43 | 7 | |||||||
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University of Barcelona; Barcelona; Spain Resource Report Resource Website |
University of Barcelona; Barcelona; Spain (RRID:SCR_002575) | UB | university | Public university in Barcelona, Spain that offers degree programs in social sciences, engineering, and arts and humanities. | public university, barcelona, spanish university, degree program |
uses: Scizzle is related to: European Gram Negative AntiBacterial Engine is parent organization of: DnaSP is parent organization of: Bellvitge Biomedical Research Institute is parent organization of: University of Barcelona Statistics and Bioinformatics Research Group is parent organization of: SerbGO is parent organization of: nucleR |
Free | nlx_21784 | SCR_002575 | SciCrunch Registry | University of Barcelona, Universitat de Barcelona | 2026-11-07 11:54:42 | 0 | |||||||
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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 | SciCrunch Registry | 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 | 2026-11-07 11:54:54 | 166 | ||||
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Triangle BioSystems Resource Report Resource Website 10+ mentions |
Triangle BioSystems (RRID:SCR_002603) | TBSI | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software | computational neuroscience, eeg, eeg, meg, electrocorticography, hardware, other software resource, physiological recording, software | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156006 | http://www.nitrc.org/projects/tbsi | SCR_002603 | SciCrunch Registry | Triangle BioSystems International | 2026-11-07 11:54:42 | 11 | ||||||
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TractoR: Tractography with R Resource Report Resource Website 10+ mentions |
TractoR: Tractography with R (RRID:SCR_002602) | TractoR | data processing software, data visualization software, software application, software resource | Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R. | analyze, atlas application, c, dicom, linux, macos, modeling, magnetic resonance, nifti, other unix-like, posix/unix-like, quantification, r, segmentation, sh, bash, statistical operation, tractography, unix shell, visualization, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_156005 | http://www.nitrc.org/projects/tractor | SCR_002602 | SciCrunch Registry | Tractography with R | 2026-11-07 11:54:54 | 28 | ||||||
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TetraMetrix Resource Report Resource Website 1+ mentions |
TetraMetrix (RRID:SCR_002601) | TetraMetrix | software resource | An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left. | magnetic resonance, 3d, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
Free, Available for download, Freely available | nlx_156004 | SCR_002601 | SciCrunch Registry | 2026-11-07 11:54:43 | 1 | ||||||||
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Template Image Processing Library Resource Report Resource Website |
Template Image Processing Library (RRID:SCR_002600) | TIPL | data processing software, image analysis software, image processing software, software application, software library, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A lightweight C++ template library designed mainly for medical imaging processing. The design paradigm follows generic programming, and the purpose is to provide an easy-to-use and also ready-to-use library. The code is template-based, and only header files are needed to be included to the source code. This library provides the following functions: # DICOM (r), Analyze(r), Nifti (r/w), and MATLAB MAT V4 (r/w) # numerical: add, multiply, gradient. # interpolation: linear, gaussian radial basis # filters: mean, gaussian, laplacian, sobel, anisotropic diffusion # morphological processing: erosion, expansion, opening, closing # template-based Fourier transform # linear coregistration: rigid body, affine transform, least square fit, mutual information # nonlinear coregistration: The Large Deformation Diffeomorphic Metric Mapping (LDDMM) | reusable library, analyze, c++, dicom, format conversion, magnetic resonance, nifti, os independent, segmentation, spatial transformation, visualization, win32 (ms windows) |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Carnegie Mellon University; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156003 | http://www.nitrc.org/projects/tipl | SCR_002600 | SciCrunch Registry | 2026-11-07 11:54:57 | 0 | |||||||
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University of Athens; Athens; Greece Resource Report Resource Website 1+ mentions |
University of Athens; Athens; Greece (RRID:SCR_002607) | UoA | university | Public university in Athens, Greece that offers degree programs in health sciences, law and economics, and theology. | public university in greece |
is related to: EARIP is related to: ORBITO is related to: International AMD Genetics Consortium is parent organization of: Digital Repository Infrastructure Vision for European Research is parent organization of: University of Athens Biophysics and Bioinformatics Laboratory |
Free | ISNI:0000 0001 2155 0800, grid.5216.0, Wikidata:Q547867, Crossref funder ID:501100005187, nlx_94434 | https://ror.org/04gnjpq42 | SCR_002607 | SciCrunch Registry | University of Athens, National and Kapodistrian University of Athens | 2026-11-07 11:54:43 | 6 | ||||||
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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 | SciCrunch Registry | TurtleSeg - Interactive 3D Image Segmentation Software | 2026-11-07 11:54:57 | 6 | ||||||
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University of Arkansas for Medical Sciences; Arkansas; USA Resource Report Resource Website 10+ mentions |
University of Arkansas for Medical Sciences; Arkansas; USA (RRID:SCR_002522) | UAMS | data or information resource, department portal, organization portal, portal | Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care. | translational medicine, public medical school |
is related to: Alzheimers Disease Genetics Consortium is related to: Clinical and Translational Science Awards Consortium has parent organization: University of Arkansas System; Arkansas; USA is parent organization of: UAMS Experimental Pathology Core Laboratory |
Free | grid.241054.6, nlx_152181, Wikidata:Q941298, Crossref funder ID:100008519, ISNI:0000 0004 4687 1637 | https://ror.org/00xcryt71 | SCR_002522 | SciCrunch Registry | University of Arkansas for Medical Sciences | 2026-11-07 11:54:40 | 41 | ||||||
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Open Journal Systems Resource Report Resource Website 1+ mentions |
Open Journal Systems (RRID:SCR_002642) | OJS | software resource | Open source software made freely available to journals worldwide for the purpose of making open access publishing a viable option for more journals, as open access can increase a journal's readership as well as its contribution to the public good on a global scale. OJS assists with every stage of the refereed publishing process, from submissions through to online publication and indexing. Through its management systems, its finely grained indexing of research, and the context it provides for research, OJS seeks to improve both the scholarly and public quality of refereed research. OJS Features # OJS is installed locally and locally controlled. # Editors configure requirements, sections, review process, etc. # Online submission and management of all content. # Subscription module with delayed open access options. # Comprehensive indexing of content part of global system. # Reading Tools for content, based on field and editors' choice. # Email notification and commenting ability for readers. # Complete context-sensitive online Help support. | journal management, publishing system, publication | is listed by: FORCE11 | Free, Available for download, Freely available | nlx_156071 | SCR_002642 | SciCrunch Registry | 2026-11-07 11:54:55 | 1 | ||||||||
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PeptideShaker Resource Report Resource Website 100+ mentions |
PeptideShaker (RRID:SCR_002520) | software resource | Software providing a search engine independent platform for visualization of peptide and protein identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data. | standalone software, proteomics, mass spectrometry, java, search engine, omssa, xtandem, mascot, ms-gf, msamanda, myrimatch, comet, tide |
is listed by: OMICtools is related to: MS Amanda has parent organization: Google Code |
PMID:34709836 | Free, Available for download, Freely available | OMICS_03347 | http://peptide-shaker.googlecode.com | SCR_002520 | SciCrunch Registry | 2026-11-07 11:54:42 | 164 |
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