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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ot-tools Resource Report Resource Website 1+ mentions |
ot-tools (RRID:SCR_017191) | software application, data processing software, data analysis software, software resource | Software tools for analysis of cellular cryo-ET data. | analysis, cellular, cryo-ET, data | Free, Available for download, Freely available | SCR_017191 | 2026-02-15 09:21:16 | 5 | |||||||||||
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BZ Analyzer software Resource Report Resource Website 10+ mentions |
BZ Analyzer software (RRID:SCR_017205) | software application, data processing software, data analysis software, software resource | Software tool as analysis application BZ-H1A by Keyence, Japan for fluorescence microscope BZ-8100 series. | analysis, BZH1A, Keyence, fluorescence, microscope | Available for purchase | SCR_017205 | 2026-02-15 09:21:59 | 13 | |||||||||||
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TopScan Resource Report Resource Website 50+ mentions |
TopScan (RRID:SCR_017141) | software application, data processing software, data analysis software, software resource | Software suite as top view based behavior analysis system by CleverSys Inc. Uses animal body parts to provide behavior analysis results. Used in experiments with animal tracking task. | top, view, behavior, analysis, system, CleverSys Inc., animal, body, part, track, detect | SCR_017141 | TopScan Suite | 2026-02-15 09:21:58 | 94 | |||||||||||
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The Cancer Genome Atlas Resource Report Resource Website 5000+ mentions |
The Cancer Genome Atlas (RRID:SCR_003193) | TCGA | material resource, biomaterial supply resource | Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments. * Genome Data Analysis Centers (GDACs) - Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data. TCGA is actively developing a network of collaborators who are able to provide samples that are collected retrospectively (tissues that had already been collected and stored) or prospectively (tissues that will be collected in the future). | genome, genome sequencing, breast, central nervous system, endocrine, gastrointestinal, gynecologic, head, neck, hematologic, skin, soft tissue, thoracic, urologic, clinical, genomic characterization, analysis, tumor genome, demographic, gene expression, copy number alteration, epigenetic, dna sequence, exome, snp, methylation, mrna, mirna, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: BioXpress is used by: cancerRxTissue is listed by: One Mind Biospecimen Bank Listing is related to: Cancer3D is related to: Cancer Research Data Commons is related to: CancerMIRNome has parent organization: National Cancer Institute works with: FireBrowse |
Cancer, Tumor, Normal, Breast cancer, Central Nervous System cancer, Endocrine cancer, Gastrointestinal cancer, Gynecologic cancer, Head cancer, Neck cancer, Hematologic cancer, Skin cancer, Soft tissue cancer, Thoracic cancer, Urologic cancer | NCI 261200800001E-12-0-1 | nlx_156913 | SCR_003193 | Cancer Genome Atlas | 2026-02-15 09:18:28 | 6292 | ||||||
|
IgBLAST Resource Report Resource Website 500+ mentions |
IgBLAST (RRID:SCR_002873) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine. | gene, analysis, domain, homology, immunoglobulin v, nucleotide, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: NCBI |
PMID:23671333 | Free, Freely available | nif-0000-25554, biotools:igblast, OMICS_06083 | https://bio.tools/igblast https://sources.debian.org/src/ncbi-igblast/ |
SCR_002873 | IgBLAST | 2026-02-15 09:18:24 | 609 | ||||||
|
QGIS Resource Report Resource Website 100+ mentions |
QGIS (RRID:SCR_018507) | software application, software resource | Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps. | Geographic information system, viewing, editing, analysis, geospatial data, spatial information analysis, graphical map, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:QGIS | https://bio.tools/QGIS | SCR_018507 | 2026-02-15 09:22:14 | 400 | ||||||||
|
MRTool Resource Report Resource Website 1+ mentions |
MRTool (RRID:SCR_015956) | data or information resource, topical portal, portal | Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. | brain, imaging, neuroimaging, analysis, magnetic, resonance, mr | requires: SPM | DOI:10.1007/s12021-018-9355-3 | Free, Available for download, Runs on MAC OS, Runs on Windows | SCR_015956 | 2026-02-15 09:21:00 | 8 | |||||||||
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Pattern Component Modelling Toolbox Resource Report Resource Website 1+ mentions |
Pattern Component Modelling Toolbox (RRID:SCR_015891) | PCM | software application, data processing software, data analysis software, software resource | Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model. | bayesian, representational, model, motor, abstract, visual, encoding, neural, imaging, activity, pattern, analysis, voxel | James McDonnell Foundation ; NSERC RGPIN-2016-04890; JSPS 15J03233 |
PMID:28843540 | Free, Available for download | SCR_015891 | Pattern component modeling (PCM), PCM Toolbox, Pattern Component Modeling toolbox for multivariate analysis | 2026-02-15 09:21:28 | 2 | |||||||
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Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | software application, data processing software, data analysis software, software resource | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | GNU Datamash | 2026-02-15 09:21:46 | 2 | |||||||
|
jamovi Resource Report Resource Website 1000+ mentions |
jamovi (RRID:SCR_016142) | software application, data processing software, data analysis software, software resource | Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience. | spreadsheet, r, statistic, methodology, r, package, analysis | Free, Available for download | SCR_016142 | the jamovi project | 2026-02-15 09:21:32 | 2851 | ||||||||||
|
FITMASTER Resource Report Resource Website 50+ mentions |
FITMASTER (RRID:SCR_016233) | software application, data processing software, data analysis software, software resource | Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series. | electrophysiology, analysis, fitting, statistic, polynomial, exponential, gaussian, boltzmann, formalism, voltage, current | Free, Available for download, Tutorial available, Demo available | SCR_016233 | HEKA FITMASTER | 2026-02-15 09:21:03 | 97 | ||||||||||
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Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | software application, data processing software, data analysis software, software resource | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-02-15 09:21:31 | 15 | |||||||
|
Mini Analysis Guide for Microarrays Resource Report Resource Website 1+ mentions |
Mini Analysis Guide for Microarrays (RRID:SCR_000596) | MAGMA | experimental protocol, data or information resource, narrative resource | A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS | microarray design, microarray, manual, guide, array, analysis, j-express, import, data processing, global analysis, differential expression, gene set, co-expressed gene |
is listed by: OMICtools has parent organization: J-Express |
OMICS_00772 | SCR_000596 | 2026-02-16 09:45:18 | 3 | |||||||||
|
EMBL - Bork Group Resource Report Resource Website |
EMBL - Bork Group (RRID:SCR_000810) | EMBL - Bork Group | laboratory portal, organization portal, portal, service resource, data or information resource | The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin. | computational biology, gene, protein, protein network, cellular process, phenotype, environment, gene, genome, metagenome, analysis, interaction, pathway, temporal, spatial, network, genotype, phenotype, molecular process |
has parent organization: European Molecular Biology Laboratory is parent organization of: SMART is parent organization of: SmashCommunity is parent organization of: Candidate Genes to Inherited Diseases |
European Molecular Biology Laboratory ; Max-Delbruck Center for Molecular Medicine ; European Union ; BMBF ; IBM |
nlx_149173 | SCR_000810 | Bork Group - Comparative Systems Analysis (EMBL) | 2026-02-16 09:45:20 | 0 | |||||||
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Biometric Research Branch: ArrayTools Resource Report Resource Website 1+ mentions |
Biometric Research Branch: ArrayTools (RRID:SCR_000778) | software application, data processing software, software toolkit, data visualization software, data analysis software, software resource | A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in. | visualization, statistic, analysis, dna, microarray, gene, expression, c, java, excel |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30199 | SCR_000778 | BRB ArrayTools | 2026-02-16 09:45:20 | 6 | ||||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-02-16 09:45:19 | 2763 | ||||
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NVM Resource Report Resource Website |
NVM (RRID:SCR_000600) | software application, data processing software, data visualization software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis. | quantitative, neuroanatomical, measurement, volumetric, image, data, draw, region, fMRI, analysis, morphology, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuromorphometrics |
NIMH R43 MH60507; NIMH R44 MH60507; NIMH R43 MH084358 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149080 | http://www.nitrc.org/projects/nvm | SCR_000600 | 2026-02-16 09:45:18 | 0 | |||||||
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University of Colorado at Boulder Labs and Facilities Resource Report Resource Website |
University of Colorado at Boulder Labs and Facilities (RRID:SCR_001054) | material service resource, analysis service resource, portal, production service resource, service resource, data or information resource | A portal for the core labs and facilities at the University of Colorado at Boulder. | electron microprobe, electron microscope, imaging, analysis, portal, labs, facilities, production service resource |
is listed by: ScienceExchange is related to: CU Boulder Electron Microprobe Laboratory is related to: CU Boulder Institute for Behavioral Genetics is related to: Colorado University Boulder BioFrontiers Advanced Light Microscopy Core Facility has parent organization: University of Colorado Boulder; Colorado; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_850 | SCR_001054 | CU Boulder Labs and Facilities, CU Boulder Labs & Facilities, University of Colorado at Boulder Labs & Facilities | 2026-02-16 09:45:24 | 0 | ||||||||
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EZ BioResearch Resource Report Resource Website 1+ mentions |
EZ BioResearch (RRID:SCR_001050) | production service resource, material service resource, reagent manufacture, service resource | A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control. | molecular biology, tool kit, dna, rna, microarray, pcr, transgenic, genotyping, analysis, biotechnology | is listed by: ScienceExchange | Commercial | SciEx_571 | http://www.scienceexchange.com/facilities/ez-bioresearch | SCR_001050 | EZ BioResearch LLC | 2026-02-16 09:45:24 | 3 | |||||||
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Connectome Mapping Toolkit Resource Report Resource Website 1+ mentions |
Connectome Mapping Toolkit (RRID:SCR_001644) | Connectome Mapping Toolkit | software application, software toolkit, data processing software, image processing software, data set, data management software, image analysis software, software resource, data or information resource | A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application. | magnetic resonance, connectome, mapping, data management, data sharing, visualization, analysis, connectome mapper, processing pipeline, python, connectomics, multi-modal, network analysis, neuroimaging, neuroinformatics tool, mri, knowledge-base, semantic, technology, mapping, source code |
is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: University of Lausanne; Lausanne; Switzerland has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland is parent organization of: Connectome Viewer |
Swiss National Science Foundation 33CM30-124089 | PMID:21713110 | Free, Available for download, Freely available | nlx_153920 | http://www.cmtk.org/ http://www.connectome.ch/ |
SCR_001644 | 2026-02-16 09:45:33 | 7 |
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