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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TomoMiner Resource Report Resource Website 1+ mentions |
TomoMiner (RRID:SCR_015045) | source code, software resource | Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging. | analysis platform, cryo electron subtomogram, subtomogram classification, subtomogram alignment, subtomogram averaging, subtomogram analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA requires: Python Programming Language requires: NumPy requires: SciPy requires: LAPACK linear algebra library requires: Cython C-Extensions for Python |
Available for download | biotools:tomominer | https://bio.tools/tomominer | SCR_015045 | 2026-08-09 09:06:31 | 3 | ||||||||
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madsim Resource Report Resource Website 1+ mentions |
madsim (RRID:SCR_014765) | source code, software resource | A function which allows users to generate two biological conditions synthetic microarray datasets. The user provides a subset of parameters, but default parameter settings can be modified. | source code, r, synthetic microarray, data set, biological condition | is related to: R Project for Statistical Computing | SCR_014765 | 2026-08-09 09:06:28 | 1 | |||||||||||
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Papaya Resource Report Resource Website 1+ mentions |
Papaya (RRID:SCR_014188) | source code, software resource | A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+). | source code, javascript, medical research, image viewer | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public, Available to the research community | https://github.com/rii-mango/Papaya/ | SCR_014188 | 2026-08-09 09:06:22 | 5 | |||||||||
|
Efficient Permutation Testing Resource Report Resource Website |
Efficient Permutation Testing (RRID:SCR_014104) | source code, software resource | A Matlab implementation for efficient permutation testing by using matrix completion. | permutation, nueroimaging, source code, fast, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Wisconsin Partnership Fund ; NIA R01 AG040396; NSF CAREER 1252725; NSF RI 1116584; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; Veterans Administration Merit Review I01CX000165 |
Available for download, Acknowledgement requested | http://pages.cs.wisc.edu/~vamsi/pt_fast.html | SCR_014104 | Speeding Up Permutation Testing in Neuroimaging | 2026-08-09 09:06:21 | 0 | |||||||
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La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care Resource Report Resource Website |
La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care (RRID:SCR_014834) | LJI DLAC; DLAC | service resource, group | The department of laboratory animal care at the La Jolla Institute for Allergy and Immunology. | laboratory animal care, research, ethics, immunology, allergy | SCR_014834 | La Jolla Institute for Allergy and Immunology DLAC, La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care (DLAC) | 2026-08-09 09:06:29 | 0 | ||||||||||
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Monkey Motion Resource Report Resource Website |
Monkey Motion (RRID:SCR_014285) | source code, software resource | A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation. | Magnetic resonance imaging, Neuroimaging, Macaca fascicularis, Operant conditioning, Reward | McDonnell Center for Systems Neuroscience at Washington University ; NINDS R01 NS044598; NIMH R21 MH081080; NIMH K24 MH087913 |
PMID:26798573 DOI:10.7759/cureus.397 |
Available for download | SCR_014285 | 2026-08-09 09:06:23 | 0 | |||||||||
|
Fast5 Library Resource Report Resource Website |
Fast5 Library (RRID:SCR_024023) | source code, software resource | Software C++ library for accessing Oxford Nanopore Technologies sequencing data. | C++ library, accessing Oxford Nanopore Technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available | OMICS_29589 | https://sources.debian.org/src/fast5/ | SCR_024023 | Fast5, fast5 | 2026-08-09 09:08:52 | 0 | |||||||
|
TADA-A Resource Report Resource Website |
TADA-A (RRID:SCR_024538) | source code, software resource | Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies. | mapping risk genes, de novo mutations, whole genome sequencing, | NIMH R01MH110531; Simons Foundation |
PMID:29754769 | Free, Available for download, Freely available | SCR_024538 | TADA-Annotations | 2026-08-09 09:08:29 | 0 | ||||||||
|
AnimalTA Resource Report Resource Website 1+ mentions |
AnimalTA (RRID:SCR_023784) | source code, software resource | Software video tracking tool for tracking and analysing animal movement in different environments. | OpenBehavior, video tracking, tracking and analysing animal movement, animal movement in different environments, | is listed by: OpenBehavior | DOI:10.1111/2041-210X.14115 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/animalta/ | SCR_023784 | Animal Tracking and Analysis | 2026-08-09 09:08:41 | 2 | |||||||
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python-biom-format Resource Report Resource Website 1+ mentions |
python-biom-format (RRID:SCR_024193) | source code, software resource | Software provides command line interface and Python API for working with Biological Observation Matrix files. | command line interface, Python API for working with Biological Observation Matrix files, BIOM files, |
is listed by: Debian is related to: biomformat |
PMID:23587224 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-biom-format/ | SCR_024193 | 2026-08-09 09:08:58 | 3 | ||||||||
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OpenSAFELY Resource Report Resource Website 10+ mentions |
OpenSAFELY (RRID:SCR_023790) | source code, software resource | The code that runs the OpenSAFELY platform used for analysis of electronic health records data. | OpenSAFELY platform, analysis of electronic health records data, | Free, Available for download, Freely available | https://www.opensafely.org/ | SCR_023790 | 2026-08-09 09:08:41 | 43 | ||||||||||
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Spatiotemporal pattern Exploration of Brain Resource Report Resource Website |
Spatiotemporal pattern Exploration of Brain (RRID:SCR_023825) | STEB | source code, software resource | Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data. | Allen Developing Mouse Brain Atlas, visual analytics, genomic and phenotypic patterns, developing mouse brain | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023825 | 2026-08-09 09:08:47 | 0 | |||||||||
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MetaPSICOV Resource Report Resource Website 1+ mentions |
MetaPSICOV (RRID:SCR_024517) | source code, software resource | Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins. | accurate prediction, contacts and long range hydrogen bonding in proteins prediction, | is listed by: SoftCite | PMID:25431331 | Free, Available for download, Freely available | SCR_024517 | 2026-08-09 09:09:04 | 2 | |||||||||
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DMS_with_Alanine_scan Resource Report Resource Website 1+ mentions |
DMS_with_Alanine_scan (RRID:SCR_023949) | source code, software resource | Code used for data processing, variant impact predictor modelling and result analysis. Used to improve prediction results to predict the impact of amino acid variants. Extended linear regression-based predictor to explore whether incorporating data from alanine scanning, widely-used low-throughput mutagenesis method, would improve prediction results. | Extended linear regression-based predictor, improve prediction results, amino acid variants impact prediction, alanine scanning data incorporation, mutagenesis method prediction results, | DOI:10.1101/2022.12.14.520494 | Free, Available for download, Freely available | SCR_023949 | 2026-08-09 09:08:20 | 1 | ||||||||||
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LinearSVC Resource Report Resource Website 1+ mentions |
LinearSVC (RRID:SCR_024741) | software application, software resource | Software application for linear support vector classification. Used in classification problems. | linear support vector classification, classification problems, | Free, Freely available | SCR_024741 | Linear Support Vector Classification | 2026-08-09 09:09:00 | 3 | ||||||||||
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SingleCellNet Resource Report Resource Website 1+ mentions |
SingleCellNet (RRID:SCR_024742) | software application, software resource | Software tool to classify single cell RNA-Seq data across platforms and across species. | classify single cell RNA-Seq data, data across platforms and across species classification, | PMID:31377170 | Free, Available for download, Freely available | SCR_024742 | 2026-08-09 09:08:32 | 2 | ||||||||||
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org.Hs.eg.db Resource Report Resource Website 10+ mentions |
org.Hs.eg.db (RRID:SCR_024739) | software toolkit, software resource | Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers. | simple mapping of Entrez Gene identifiers, GenBank accession numbers, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024739 | 2026-08-09 09:08:32 | 45 | ||||||||||
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MCFLIRT Resource Report Resource Website 1+ mentions |
MCFLIRT (RRID:SCR_024792) | software application, software resource | Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration. | registration for brain images, medical image analysis, motion correction, | is a plug in for: FSL | Free, Freely available | SCR_024792 | Motion Correction FMRIB's Linear Image Registration Tool, , MC FMRIB's Linear Image Registration Tool | 2026-08-09 09:08:33 | 4 | |||||||||
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SlicerMorph Resource Report Resource Website 1+ mentions |
SlicerMorph (RRID:SCR_024674) | source code, software resource | Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application. | retrieve, visualize, analyse 3D morphology, import microCT data extension, data import, visualization, measurement, annotation, geometric morphometric analysis, 3D data, volumetric scans, 3D surface scans | works with: 3D Slicer | NSF Advances in Biological Informatics | DOI:10.1111/2041-210X.13669 | Free, Available for download, Freely available | SCR_024674 | 2026-08-09 09:09:05 | 3 | ||||||||
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rpy2 Resource Report Resource Website 10+ mentions |
rpy2 (RRID:SCR_024701) | source code, software resource | Software interface to use R from Python. | interface, R, Python | https://github.com/rpy2/rpy2 | SCR_024701 | 2026-08-09 09:08:31 | 11 |
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