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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | data or information resource, disease-related portal, portal, topical portal | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NCRR M01 RR00080; NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-09-05 06:28:11 | 4 | ||||||
|
SPM U+ Resource Report Resource Website 1+ mentions |
SPM U+ (RRID:SCR_016743) | SPM U+ | data analysis software, data processing software, software application, software resource, software toolkit | Software Project Management (SPM) tools which contain a collection of functions that can be used at different stage of a standard massive univariate fMRI data analysis. Used to improve mass univariate analysis. | SPM, standard, massive, univariate, plus, data, fMRI, analysis | Free, Available for download, Freely available | https://osf.io/wn3h8/ | SCR_016743 | , Software Project Management Univariate Plus, SPM Univariate Plus, SPM U+, Software Project Management U+ | 2026-09-05 06:28:13 | 5 | ||||||||
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Rampart Resource Report Resource Website 1+ mentions |
Rampart (RRID:SCR_016742) | data processing software, software application, software resource, workflow software | Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems. | workflow, management, system, de novo, genome, assembly, DNA, sequence, data, high, performance, computing, environment, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: The Genome Analysis Centre; Norwich; United Kingdom |
BBSRC | PMID:25637556 | Free, Available for download, Freely available | biotools:rampart | http://www.earlham.ac.uk/rampart/, https://bio.tools/rampart | SCR_016742 | 2026-09-05 06:28:13 | 2 | ||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data analysis software, data processing software, software application, software resource | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-09-05 06:28:16 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | alignment software, data analysis software, data processing software, image analysis software, software application, software resource | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian Government ; Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-09-05 06:28:16 | 203 | ||||||
|
scran Resource Report Resource Website 100+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, data processing software, software application, software resource | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; EMBL ; National Health and Medical Research Council of Australia |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-09-05 06:28:16 | 100 | ||||
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OptiQuant Software Resource Report Resource Website 1+ mentions |
OptiQuant Software (RRID:SCR_016769) | data acquisition software, data analysis software, data processing software, image acquisition software, image analysis software, software application, software resource | Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer. | image, acquisition, analysis, display, archiving, quantify, autoradiography, data, PerkinElmer | Commercially available, Free download available | https://optiquant.software.informer.com/5.0/ | SCR_016769 | OptiQuant, OptiQuant 3.0, OptiQuant software 5.0, OptiQuant 5.0 | 2026-09-05 06:28:14 | 4 | |||||||||
|
mixOmics Resource Report Resource Website 50+ mentions |
mixOmics (RRID:SCR_016889) | data analysis software, data processing software, software application, software resource | Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multivariate, exploration, integration, biological, dataset, variable, selection, analysis, data, high, throughput, sequencing, technology, spectral, imaging |
is related to: R Project for Statistical Computing has parent organization: University of Melbourne; Victoria; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016889 | 2026-09-05 06:28:15 | 61 | ||||||||||
|
BISE Resource Report Resource Website 10+ mentions |
BISE (RRID:SCR_016774) | analysis service resource, data or information resource, database, organization portal, portal, production service resource, service resource, software resource | Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows. | bioimage, analysis, data, information, image, processing, algorithm, workflow, bio.tools |
lists: FibrilTool is listed by: Debian is listed by: bio.tools has parent organization: NEUBIAS |
Free, Freely available, Registration required | biotools:BISE | https://bio.tools/BISE | SCR_016774 | 2026-09-05 06:28:14 | 13 | ||||||||
|
Tools for NIfTI and ANALYZE image Resource Report Resource Website 1+ mentions |
Tools for NIfTI and ANALYZE image (RRID:SCR_016895) | data analysis software, data processing software, image analysis software, service resource, software application, software resource, software toolkit | Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform. | neuroimaging, data, program, analysis, image |
is related to: NIfTI Data Format Working Group is related to: MATLAB |
Free, Available for download, Freely available | https://perso.telecom-paristech.fr/bloch/P6Image/Projets/Nez2/NIfTI_matlab_tools/NIfTI_tools.pdf | SCR_016895 | Neuroimaging Informatics Technology Initiative (NIfTI) and Analyze Image data | 2026-09-05 06:28:15 | 1 | ||||||||
|
FlowSOM Resource Report Resource Website 100+ mentions |
FlowSOM (RRID:SCR_016899) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. | flow, cytometry, data, analysis, self, organizing, map, marker, cell, detect, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing is a plug in for: FlowJo |
PMID:25573116 | Free, Available for download, Freely available | biotools:flowsom | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html, https://www.flowjo.com/exchange/#/plugin/profile?id=7, https://bio.tools/flowsom | SCR_016899 | FlowSOM, Flow Self Organizing Map | 2026-09-05 06:28:15 | 125 | ||||||
|
FRETBursts Resource Report Resource Website 1+ mentions |
FRETBursts (RRID:SCR_016898) | FRETBursts | data analysis software, data processing software, software application, software resource, software toolkit | Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data. | freely, diffusing, single, molecule, FRET, smFRET, cellular, process, intermolecular, interaction, conformational, change, biomacromolecule, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM069709; NIGMS R01 GM95904 |
PMID:27532626 | Free, Available for download, Freely available | biotools:fretbursts | https://opensmfs.github.io/FRETBursts/, https://bio.tools/fretbursts | SCR_016898 | Förster Resonance Energy Transfer Bursts, FRETBursts | 2026-09-05 06:28:15 | 3 | ||||
|
CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | data analysis software, data processing software, image analysis software, software application, software resource | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-09-05 06:28:15 | 18 | ||||||||
|
dcmqi Resource Report Resource Website 1+ mentions |
dcmqi (RRID:SCR_016933) | dcmqi | data processing software, image processing software, software application, software library, software resource, software toolkit | Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. | DICOM, converter, medical, image, computing, quantitative, analysis, clinical, data, metadata, radiology, standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Harvard University; Cambridge; United States |
NCI U24 CA180918; NIBIB P41 EB01589; NIBIB P41 EB015902; NIBIB R01 EB014955 |
PMID:29092948 | Free, Available for download, Freely available, Tutorial available | biotools:dcmqi | https://github.com/QIICR/dcmqi, https://bio.tools/dcmqi | SCR_016933 | DICOM for Quantitative Imaging, The Digital imaging and Communications in Medicine for Quantitative Imaging, Digital imaging and Communications in Medicine for Quantitative Imaging, DCMQI | 2026-09-05 06:28:15 | 4 | ||||
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Wizard Resource Report Resource Website 1+ mentions |
Wizard (RRID:SCR_016939) | data analysis software, data processing software, software application, software resource | Software tool for data analysis and exploration. Statistics software for Mac. | statistics, software, Mac, data, analysis | Commercially available, Free trial available, Tutorial available | https://www.macupdate.com/app/mac/50415/wizard | SCR_016939 | Wizard 1.9.28, Wizard 1.9.27, Wizardmac | 2026-09-05 06:28:15 | 6 | |||||||||
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International Human Epigenome Consortium Resource Report Resource Website 10+ mentions |
International Human Epigenome Consortium (RRID:SCR_016937) | IHEC | consortium, data or information resource, organization portal, portal | Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal. | reference, human, epigenome, map, normal, disease, cell, data, quality, standard, sharing |
is related to: 4D Nucleome is related to: Canadian Epigenetics, Environment and Health Research Consortium Network is parent organization of: International Human Epigenome Consortium Data Portal |
Free access to the research community, Open and controlled access to datasets according to policies and guidelines | https://epigenomesportal.ca/ihec/ | SCR_016937 | International Human Epigenome Consortium, IHEC | 2026-09-05 06:28:15 | 34 | |||||||
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XDSME Resource Report Resource Website 10+ mentions |
XDSME (RRID:SCR_016943) | xdsme | data processing software, image processing software, software application, software resource, software toolkit | Software package of python scripts made to simplify the processing of crystal diffraction images. | simplify, processing, crystal, diffraction, image, data, XDS |
uses: Python Programming Language works with: XDS Program Package |
Free, Available for download, Freely available | SCR_016943 | XDSME, X-ray Detector Software Made Easier, XDS Made Easier | 2026-09-05 06:28:16 | 15 | ||||||||
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Neurolucida 360 Resource Report Resource Website 10+ mentions |
Neurolucida 360 (RRID:SCR_016788) | data analysis software, data processing software, software application, software resource | Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses. | mbf Bioscience, automatic, image, 3D, reconstruction, analysis, neuron, synapse, data | is used by: SPARC Portal | Commercially available, Free trial available | SCR_016788 | 2026-09-05 06:28:14 | 49 | ||||||||||
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NetworkAnalyst Resource Report Resource Website 500+ mentions |
NetworkAnalyst (RRID:SCR_016909) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, network analysis software, production service resource, service resource, software application, software resource, web service | Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data. | gene, expression, profiling, meta, data, analysis, statistical, visual, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25950236 | Free, Freely available, Tutorial available | biotools:networkanalyst | https://bio.tools/networkanalyst | SCR_016909 | 2026-09-05 06:28:15 | 975 | |||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | data analysis software, data processing software, software application, software resource | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIDA P30 DA018310; NIGMS R01 GM067193 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-09-05 06:28:15 | 14 |
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