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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-09-12 01:02:22 | 0 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software application, software resource | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-09-12 01:02:27 | 301 | ||||||
|
SPHARM-PDM Toolbox Resource Report Resource Website |
SPHARM-PDM Toolbox (RRID:SCR_002546) | SPHARM-PDM Toolbox | software application, software resource | Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures. | analyze, c++, console (text based), macos, microsoft, magnetic resonance, nifti, nrrd, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: National Alliance for Medical Image Computing has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:24027625 | Free, Available for download, Freely available | nlx_155953 | http://www.nitrc.org/projects/spharm-pdm | SCR_002546 | UNC SPHARM-PDM, SPHARM-PDM UNC Toolbox | 2026-09-12 01:02:28 | 0 | |||||
|
scikit-learn Resource Report Resource Website 10000+ mentions |
scikit-learn (RRID:SCR_002577) | scikit-learn | software application, software resource | scikit-learn: machine learning in Python | algorithm, discriminant analysis, independent component analysis, linear, macos, microsoft, modeling, magnetic resonance, nonlinear, posix/unix-like, principal component analysis, python, regression, statistical operation, windows, data mining, data analysis, classification, clustering, dimensionality reduction, model selection, preprocessing, machine learning | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:24600388 | Free, Available for download, Freely available | nlx_155979 | http://www.nitrc.org/projects/scikit-learn | SCR_002577 | scikit-learn: machine learning in Python | 2026-09-12 01:02:28 | 14714 | |||||
|
VR Worlds 2 Resource Report Resource Website |
VR Worlds 2 (RRID:SCR_002608) | VR Worlds 2 | commercial organization, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. NOTE: VR Worlds 2 is no longer available as a standalone software. Software application designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate, real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs. Create complex environments with meaningful content using VR Worlds 2?s user-friendly, drag-and-drop interface. Include triggers to launch simple or intricate events, such as a conversation between characters or a customizable rating scale. VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments, including: * Residential/Urban Area * Hotel Lobby * Medical Office * Grocery Store * Neighborhood for drug and alcohol cue extinction treatment (featured on GMA, motion capture process) * Casino for gambling addiction research (featured on Canadian Discovery Channel) * Driving simulation for mild cognitive impairment research * Phobia scenarios * Spatial navigation mazes | eeg, meg, electrocorticography, experimental control, microsoft, magnetic resonance, win32 (ms windows), windows, windows vista, windows xp, neurobehavior, virtual environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156011 | http://www.nitrc.org/projects/vr2 | SCR_002608 | 2026-09-12 01:02:29 | 0 | |||||||
|
Psychophysics Toolbox Resource Report Resource Website 1000+ mentions |
Psychophysics Toolbox (RRID:SCR_002881) | PTB, PTB-3, PTB-2 | software resource, software toolkit | A free set of Matlab and GNU/Octave functions for vision research. It makes it easy to synthesize and show accurately controlled visual and auditory stimuli and interact with the observer. | matlab, gnu/octave, vision, visual, auditory, stimuli, mac osx, linux, windows | Free, Freely available, Available for download | rid_000041 | SCR_002881 | Psychtoolbox, Psychtoolbox-3 | 2026-09-12 01:02:29 | 1139 | ||||||||
|
DNAPlotter Resource Report Resource Website 100+ mentions |
DNAPlotter (RRID:SCR_005006) | DNAPlotter | software application, software resource | Software application used to generate images of circular and linear DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3. | java, circular, linear, plot, genome, macosx, unix, windows |
is listed by: OMICtools is related to: Artemis: Genome Browser and Annotation Tool has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:18990721 | GNU General Public License | OMICS_00906, nlx_96278 | SCR_005006 | DNAPlotter: circular and linear interactive genome visualization | 2026-09-12 01:02:34 | 110 | ||||||
|
BrainCSI Resource Report Resource Website 1+ mentions |
BrainCSI (RRID:SCR_013244) | BrainCSI | data processing software, image analysis software, software application, software resource | A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images. | magnetic resonance spectroscopy, c++, console (text based), dicom, macos, microsoft, magnetic resonance, nifti, posix/unix-like, software, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
BSD License | nlx_155711 | http://www.nitrc.org/projects/braincsi | SCR_013244 | 2026-09-12 01:01:01 | 1 | |||||||
|
PsychoPy Resource Report Resource Website 1000+ mentions |
PsychoPy (RRID:SCR_006571) | PsychoPy | software application, software resource | Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime. | console (text based), experimental control, freebsd, linux, macos, microsoft, magnetic resonance, posix/unix-like, python, win32 (ms windows), windows, neuroscience, psychology, psychophysics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: University of Nottingham; Nottingham; United Kingdom |
PMID:17254636 PMID:19198666 |
GNU General Public License | nlx_155928 | http://www.nitrc.org/projects/psychopy, https://sources.debian.org/src/psychopy/ | SCR_006571 | PsychoPy - Psychology software in Python | 2026-09-12 01:02:36 | 2245 | |||||
|
Marker And Gene Interpolation and Correlation Resource Report Resource Website 10+ mentions |
Marker And Gene Interpolation and Correlation (RRID:SCR_009268) | MaGIC | software application, software resource | Software program to generate targeted marker sets for genome-wide association studies. | gene, genetic, genomic, microsoft visual foxpro, windows |
is listed by: Genetic Analysis Software has parent organization: King's College London; London; United Kingdom |
PMID:15597550 | Free, Public | nlx_154448 | SCR_009268 | Marker And Gene Interpolation and Correlation | 2026-09-12 01:02:43 | 10 | ||||||
|
mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | data processing software, software application, software resource | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-09-12 01:00:52 | 0 | ||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-09-12 01:00:33 | 0 | ||||||
|
Datavyu Resource Report Resource Website 50+ mentions |
Datavyu (RRID:SCR_003587) | Datavyu | software application, software resource, source code | Free, Java-based video coding and data visualization tool for collecting behavioral data from video. It supports all video formats that Quicktime or VLC can play, including .asf, .wmv, .avi, .flv, .mov, .mpf, .ogg, .mpg, .nsc, .wav, and .dts. It exports data in a variety of forms depending on analysis needs. | windows, mac os, java, video coding, behavior, visualization |
is related to: Databrary is related to: Databrary has parent organization: New York University; New York; USA |
GNU General Public License, v3 | nlx_157734 | SCR_003587 | 2026-09-12 01:01:29 | 79 | ||||||||
|
PANDAseq Resource Report Resource Website 500+ mentions |
PANDAseq (RRID:SCR_002705) | software resource, source code | Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. | standalone software, unix/linux, mac os x, windows, c | is listed by: OMICtools | PMID:22333067 | Free, Available for download, Freely available | OMICS_05255 | SCR_002705 | PAired-eND Assembler for DNA sequences | 2026-09-12 01:03:13 | 720 | |||||||
|
FastPCR Resource Report Resource Website 50+ mentions |
FastPCR (RRID:SCR_003155) | FastPCR | commercial organization, software resource | Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching. | probe design, probe, windows, pcr primer | is listed by: OMICtools | PMID:24395370 | Free, Available for download, Freely available | OMICS_02336 | SCR_003155 | 2026-09-12 01:03:13 | 93 | |||||||
|
FinchTV Resource Report Resource Website 500+ mentions |
FinchTV (RRID:SCR_005584) | FinchTV | commercial organization, software resource | Chromatogram viewer that can display an entire trace in a scalable multi-pane view, allows raw data views, BLAST searching and the ability to reverse complement sequences and traces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chromatogram, linux, mac osx, windows, solaris, dna sequence trace, dna sequence, trace |
is listed by: OMICtools has parent organization: Geospiza |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01019 | SCR_005584 | FinchTV - A Brilliant Trace Viewer | 2026-09-12 01:03:15 | 646 | |||||||
|
VectorFriends Resource Report Resource Website |
VectorFriends (RRID:SCR_001230) | VectorFriends | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists. | cloning, isothermal assembly, pcr, primer design, data management, sequence analysis, sequence, analysis, primer, windows, mac os | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02113 | SCR_001230 | 2026-09-12 01:03:11 | 0 | ||||||||
|
SNPP Resource Report Resource Website 50+ mentions |
SNPP (RRID:SCR_009404) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. A dynamic general database management system to manage high-throughput SNP genotyping data. It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system. | gene, genetic, genomic, java, windows, linux, solaris, macos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154648 | SCR_009404 | Single Nucleotide Polymorphism Processor | 2026-09-12 01:02:46 | 60 | ||||||||
|
E-Prime Extensions for fMRI Resource Report Resource Website |
E-Prime Extensions for fMRI (RRID:SCR_009568) | EEfMRI | software application, software resource | Software designed to optimize E-Prime experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime. | experimental control, microsoft, magnetic resonance, win32 (ms windows), windows, windows vista, windows xp, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Other/Commercial license License | nlx_155748 | http://www.nitrc.org/projects/eefmri | SCR_009568 | 2026-09-12 01:02:47 | 0 | |||||||
|
fMRI-CPCA Resource Report Resource Website 1+ mentions |
fMRI-CPCA (RRID:SCR_009520) | fMRI-CPCA, fMRI CPCA | software application, software resource | Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline. CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated. | analyze, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, principal component analysis, regression, statistical operation, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155682 | SCR_009520 | fMRI-Constrained Principal Component Analysis, fMRI Constrained Principal Component Analysis | 2026-09-12 01:02:46 | 7 |
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