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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ShinyLearner Resource Report Resource Website 1+ mentions |
ShinyLearner (RRID:SCR_017608) | data analysis software, software resource, data processing software, software application | Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data. | Benchmark, machine, learning, classification, algorithm, tabular, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/675181 | Free, Available for download, Freely available | biotools:ShinyLearner | https://bio.tools/ShinyLearner | SCR_017608 | 2026-02-14 02:03:14 | 2 | |||||||
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Silver Lab Microscopy Software Resource Report Resource Website 1+ mentions |
Silver Lab Microscopy Software (RRID:SCR_017456) | data visualization software, data processing software, data acquisition software, software application, software resource | Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system. | Imaging, visualising, electrophysiological, data, acousto, optic, lens, microscope, Silver Lab, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University College London; London; United Kingdom |
NINDS NS099689 | Free, Available for download, Freely available | http://silverlab.org/software-resources/ | SCR_017456 | 2026-02-14 02:03:25 | 2 | ||||||||
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vbSPT Resource Report Resource Website 1+ mentions |
vbSPT (RRID:SCR_017554) | data analysis software, software resource, data processing software, software application | Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants. | Analysis, single, particle, diffusion, trajectory, Markov, short, molecule, intracellularly, protein, data, transition, state | PMID:23396281 | Free, Available for download, Freely available | https://sourceforge.net/projects/vbspt/files/latest/download?source=files | SCR_017554 | variational Bayes single particle tracking | 2026-02-14 02:03:29 | 3 | ||||||||
|
LabChart Reader Resource Report Resource Website 100+ mentions |
LabChart Reader (RRID:SCR_017551) | data analysis software, software resource, data processing software, software application | LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis. | Adinstruments, LabChart, data, analysis, calculation, plot | is related to: LabChart | https://www.adinstruments.com/products/labchart/versions-and-licenses | SCR_017551 | LabChart Reader software 8.1, LabChart Reader software | 2026-02-14 02:03:26 | 141 | |||||||||
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Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | data repository, storage service resource, data or information resource, service resource, database | Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. | Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior |
is listed by: Debian is listed by: bio.tools is listed by: OpenBehavior has parent organization: Western University; Ontario; Canada |
Weston Brain Institute (Canada) ; Canadian Institute of Health Research ; NSERC ; Alzheimer’s Society of Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Brain Canada |
PMID:31825307 | Free, Freely available | SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes | https://bio.tools/MouseBytes https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/ https://doi.org/10.17616/R31NJN7I |
SCR_017904 | MouseBytes | 2026-02-14 02:03:28 | 4 | |||||
|
Drishti Resource Report Resource Website 10+ mentions |
Drishti (RRID:SCR_017999) | data visualization software, software resource, data processing software, software application | Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc. | Visualization, volumetric data, tomography, electron microscopy, data | Free, Available for download, Freely available | SCR_017999 | 2026-02-14 02:03:29 | 19 | |||||||||||
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VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | data visualization software, data processing software, data analysis software, software application, software resource | Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data. | Computed tomography, CT, data, analysis, processing, 3D, visualization, CT data | Restricted | SCR_017997 | VGStudio MAX, VG Studio MAX 3.1, VGStudio | 2026-02-14 02:03:31 | 11 | ||||||||||
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webchem Resource Report Resource Website 1+ mentions |
webchem (RRID:SCR_017684) | software resource, data processing software, data acquisition software, software application | Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information. | R programming language, acquire, chemical, information, online, data, retrive | is listed by: CRAN | Free, Available for download, Freely available | https://docs.ropensci.org/webchem/ https://github.com/ropensci/webchem |
SCR_017684 | Chemical Information from Web | 2026-02-14 02:03:23 | 1 | ||||||||
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LibreOfficeCalc Resource Report Resource Website 10+ mentions |
LibreOfficeCalc (RRID:SCR_018013) | data visualization software, data processing software, data management software, data analysis software, software application, software resource | Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation. | Data, analysis, spreadsheet, template, process, visualize | Free, Available for download, Freely available | SCR_018013 | 2026-02-14 02:03:29 | 24 | |||||||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | data processing software, data analysis software, software toolkit, software application, software resource | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-02-14 02:03:15 | 2 | |||||
|
CNV webstore Resource Report Resource Website 1+ mentions |
CNV webstore (RRID:SCR_018007) | data visualization software, data processing software, data storage software, data analysis software, software toolkit, software application, software resource | Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. | Copy number variation, data, Illumina, CNV report, raw data, microarray data, clinical, analysis, visualization, gene prioritisation, PubMed searching, annotation, | Belgian National Fund for Scientific Research - Flanders ; Marguerite-Marie Delacroix foundation |
PMID:21208430 | http://cnv-webstore.ua.ac.be/cnv-webstore/ | SCR_018007 | CNV-webstore, CNV-WebStore | 2026-02-14 02:03:29 | 1 | ||||||||
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MicroDynamix Resource Report Resource Website 1+ mentions |
MicroDynamix (RRID:SCR_017671) | data processing software, software application, software resource, image reconstruction software, image analysis software | Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison. | MBF Bioscience, dendritic, spine, analysis, visualize, quantify, morphology, image, data, 3D, reconstruct | Restricted | SCR_017671 | 2026-02-14 02:03:23 | 1 | |||||||||||
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Vesalius Resource Report Resource Website |
Vesalius (RRID:SCR_017670) | data processing software, data acquisition software, image acquisition software, software application, software resource, image analysis software | Software tool as ultra fast, multi channel resonant scanning laser confocal microscope system for rapid 2D and 3D slide scanning, and cleared tissue imaging. System for imaging of slide mounted specimens and cleared tissue imaging. Utilizes strip mosaic scanning process to rapidly and accurately collect fluorescent image data while stage moves specimen continuously in y-axis. | MBF Bioscience, resonant, scanning, laser, confocal, microscope, system, 2D, 3D, slide, cleared, tissue, imaging, collect, fluorescent, image, data, | Restricted | SCR_017670 | 2026-02-14 02:03:28 | 0 | |||||||||||
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Nextstrain Resource Report Resource Website 100+ mentions |
Nextstrain (RRID:SCR_018223) | data set, data or information resource, portal, project portal | Open source project to harness scientific and public health potential of pathogen genome data. Provides continually updated view of publicly available data alongside powerful analytic and visualization tools for use by community. Used to aid epidemiological understanding and improve outbreak response. Open source SARS-CoV-2 genome data and analytic and visualization tools. | Pathogen genome data, data, analytic tool, visualization tool, epidemiology, outbreak response |
is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Global Initiative on Sharing All Influenza Data |
COVID-19 | Free, Freely available | https://nextstrain.org/ncov/global | SCR_018223 | nextstrain.org | 2026-02-14 02:03:35 | 273 | |||||||
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Allen Software Development Kit Resource Report Resource Website 10+ mentions |
Allen Software Development Kit (RRID:SCR_018183) | AllenSDK | data analysis software, software resource, data processing software, software application | Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas. | Data analysis, data processing, Allen Brain Atlas, data, brain |
is related to: Allen Brain Atlas is organization facet of: BICCN |
Free, Freely available | SCR_018192 | https://allensdk.readthedocs.io/en/latest/ | SCR_018183 | 2026-02-14 02:03:34 | 28 | |||||||
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NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | data access protocol, software resource, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ |
SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-02-14 02:03:28 | 138 | |||||
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IMGT Repertoire Resource Report Resource Website 10+ mentions |
IMGT Repertoire (RRID:SCR_018220) | data or information resource | Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system. | LIGM data, immunoglobulins, T cell receptor, histocompatibility, protein, immune system, data | is related to: IMGT - the international ImMunoGeneTics information system | Free, Freely available | SCR_018220 | IMGT Repertoire (MH), Repertoire (IG and TR), IMGT Repertoire (RPI), ImMunoGeneTics Repertoire | 2026-02-14 02:03:18 | 10 | |||||||||
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Velocyto Resource Report Resource Website 100+ mentions |
Velocyto (RRID:SCR_018167) | data analysis software, software resource, data processing software, software application | Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R. | Expression dynamic, single cell RNAseq data, data, RNAseq, RNA velocity, mRNA, RNAseq dataset, estimation RNA velocity | Free, Available for download, Freely available | https://github.com/velocyto-team/velocyto.py https://github.com/velocyto-team/velocyto.R |
SCR_018167 | velocyto.py, velocyto, velocyto.R | 2026-02-14 02:03:17 | 137 | |||||||||
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astroML Resource Report Resource Website |
astroML (RRID:SCR_018138) | data visualization software, data processing software, data set, data or information resource, data analysis software, software toolkit, software application, software resource | Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics. | Machine learning, statistics, data mining, data, astronomy, astrophysics, data analysis | DOI:10.1109/CIDU.2012.6382200 | Free, Available for download, Freely available | https://github.com/astroML/astroML/blob/master/doc/index.rst | SCR_018138 | 2026-02-14 02:03:31 | 0 | |||||||||
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SnapTools Resource Report Resource Website 10+ mentions |
SnapTools (RRID:SCR_018097) | SnapTools | data processing software, alignment software, software application, software resource, image analysis software | Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets. | Sequence, snap file, single nucleus, ATACseq dataset, data | is used by: scATAC Pipeline | Free, Available for download, Freely available | SCR_018097 | Single Nucleus Accessibility Profile Tools, Single nucleus accessibility profile Tools | 2026-02-14 02:03:33 | 14 |
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