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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Leica Application Suite X Resource Report Resource Website 500+ mentions |
Leica Application Suite X (RRID:SCR_013673) | LAS X | resource | Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes. | confocal, image, analysis, leica, microscope, microbiology | has parent organization: Leica Microsystems | Commercially available | http://www.leica-microsystems.com/products/microscope-software/software-for-life-science-research/las-easy-and-efficient/ | SCR_013673 | Leica LAS, Leica LAS AF Image Acquisition Software, Leica Application Suite X, Leica Application Suite X (LAS X), Leica LAS X Life Science Microscope Software, Leica LAS X LS, LASX, Leica LAS X Life Science software, LAS X | 2026-07-25 12:07:54 | 526 | |||||||
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Thermo Fisher: GeneChip� Scanner 3000 7G Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk, https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-07-25 12:08:19 | 1 | |||||||||
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NZYTech Resource Report Resource Website 10+ mentions |
NZYTech (RRID:SCR_016772) | organization | Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins. | biomaterial, analysis, service, production, supplier, molecular, biology, diagnostics, enzyme, protein | grid.436825.e, Wikidata: Q30291029 | https://ror.org/00rtryt44 | SCR_016772 | Lda. � Genes and Enzymes, NZYTech | 2026-07-25 12:08:28 | 11 | |||||||||
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BioNano: Irys system Resource Report Resource Website 10+ mentions |
BioNano: Irys system (RRID:SCR_016754) | instrument resource | System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies. | instrument, Irys, system, BioNano Genomics, BioNanomatrix, optical, next, generation, mapping, sequence, assembly, structural, variation, analysis, data, | Commercially available | https://bionanogenomics.com/wp-content/uploads/2017/01/2016-Irys-System-Brochure.pdf | https://bionanogenomics.com/technology/genome-assembly/ | SCR_016754 | 2026-07-25 12:08:25 | 35 | |||||||||
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Scanco: Medical microCT 100 system Resource Report Resource Website 1+ mentions |
Scanco: Medical microCT 100 system (RRID:SCR_017119) | instrument resource | Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG. | SCANCO, micro, CT, computed, tomography, scanner, 3D, imaging, speciment, in vitro, analysis, visualization, image, data | Available for purchase | https://www.scanco.ch/images/Brochures/microct-v16.pdf | http://www.scanco.ch/en/systems-solutions/specimen/microct100.html | SCR_017119 | 2026-07-25 12:08:32 | 7 | |||||||||
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Agilent: G2565CA Microarray Scanner Resource Report Resource Website 1+ mentions |
Agilent: G2565CA Microarray Scanner (RRID:SCR_017206) | instrument resource | Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays. | microarray, analysis, Agilent, scanner, slide, fluorescence, intensity, nucleic, acid, sample | Available for purchase | SCR_019384, Model_Number_2565CA | https://www.agilent.com/cs/library/usermanuals/Public/G2505-90019_ScannerC_User.pdf | https://www.chem-agilent.com/contents.php?id=1000947 | SCR_017206 | 2026-07-25 12:08:31 | 1 | ||||||||
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BPC Instruments: Biomethane Potential Test Resource Report Resource Website |
BPC Instruments: Biomethane Potential Test (RRID:SCR_017319) | BMP, BMP Test, AMPTS | instrument resource | Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry. | Anaerobic digestion, waste to energy, waste management, renewable energies, biogas, biomethane, modelling, University of Johannesburg (UJ), UJ-PEETS, Quantification, characterization, analysis, AI-2 import system permease protein lsrC | has parent organization: University of Johannesburg; Johannesburg; South Africa | TIA ; DST ; WRC ; NRF ; UNESCO ; SME |
https://www.uj.ac.za/faculties/febe/peets | SCR_017319 | , Automatic Methane Potential Test System (AMPTS) II, Biomethane Potential Test System, Automatic Methane Potential Test System | 2026-07-25 12:08:33 | 0 | |||||||
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Brainreader Resource Report Resource Website 1+ mentions |
Brainreader (RRID:SCR_017308) | software resource | Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain. | Company, Denmark, medical, image, analysis, processing, software, brain | is affiliated with: Neuroreader | SCR_017308 | brainreader, BrainReader | 2026-07-25 12:08:36 | 3 | ||||||||||
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Interact Resource Report Resource Website 1+ mentions |
Interact (RRID:SCR_019254) | software resource | Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software. | Synchronized viewing, analysis, video footage, audio files, observational research, video coding | Restricted | SCR_019254 | 2026-07-25 12:09:06 | 5 | |||||||||||
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Molecular Devices: Molecular Dynamics Storm 860 Molecular Imager Resource Report Resource Website |
Molecular Devices: Molecular Dynamics Storm 860 Molecular Imager (RRID:SCR_018032) | instrument resource | Multifunction phosphoimager fluorimager laser scanner that collects fluorescent or storage phosphor images from gels, membranes and phosphor screens. It is equipped with blue (450 nm) and red (635 nm) lasers, can scan at resolutions down to 50 microns. It is able to quantify radioactive gels for commonly used isotopes such as 32P, 33P, 125I, 35S, and 14C. There are three detection modes: phosphor screen mode, red/blue fluorescence, chemifluorescence. | ABRF, molecular imager, GE HealthCare, gel, blot, analysis, laser scanner, instrument, equipment | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018032.pdf | Model_Number_Storm 860 Imager | https://btiscience.org/wp-content/uploads/2014/04/Storm_User_Manual.pdf | https://www.mbl.edu/jbpc/files/2014/05/Storm_Info.pdf | SCR_018032 | Storm 860 Molecular Imager, Storm Gel and Blot Imaging System | 2026-07-25 12:08:41 | 0 | ||||||
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GE: Phoenix Nanotom S Resource Report Resource Website 1+ mentions |
GE: Phoenix Nanotom S (RRID:SCR_017995) | instrument resource | System for scientific and industrial nanofocus computed tomography nanoCT and 3D metrology. Realizes unique spatial and contrast resolution on wide sample and application range. Used in material science, precision injection moulding, micromechanics, electronics geology and biology. Used in 3D CT applications. Allows many analysis, e.g. non-destructive visualization of slices, arbitrary sectional views, or automatic pore analysis. | NanoCT, 3D, 3D CT application, spatial, contrast resolution, analysis, non-destructive visualization, slice, section, pore analysis, nanofocus computed tomography | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_017995.pdf | https://www.rcon-ndt.com/products/radiography/x-ray-systems/phoenix-nanotom-s/ | SCR_017995 | 2026-07-25 12:08:40 | 1 | |||||||||
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GenomeJack Resource Report Resource Website 10+ mentions |
GenomeJack (RRID:SCR_012026) | GenomeJack | software resource | A genome browser specialized in next-generation sequencing data. | next-generation sequencing, genome, browser, analysis | is listed by: OMICtools | Free, Public | OMICS_02143 | SCR_012026 | 2026-07-25 12:07:25 | 32 | ||||||||
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Golden Helix Incorporated Resource Report Resource Website 100+ mentions |
Golden Helix Incorporated (RRID:SCR_012191) | Golden Helix | commercial organization | Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine. | resource, portal, analysis, software |
is listed by: ScienceExchange is parent organization of: Golden Helix GenomeBrowse is parent organization of: SNP and Variation Suite SNP Analysis is parent organization of: SNP and Variation Suite CNV Analysis is parent organization of: SNP and Variation Suite |
Available to external user | SciEx_10349 | http://www.goldenhelix.com/Services, http://www.scienceexchange.com/facilities/golden-helix-inc | SCR_012191 | Golden Helix Inc., GoldenHelix.com | 2026-07-25 12:07:30 | 138 | ||||||
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SGD Resource Report Resource Website 1000+ mentions |
SGD (RRID:SCR_004694) | SGD, SGD LOCUS, SGD REF | database, data or information resource | A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available. | database, yeast, pathway, analysis, gene, nomenclature, predicted sequence, fungi, functional relationship, protein structure, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: PhenoGO is listed by: re3data.org is listed by: OMICtools is listed by: InterMOD is listed by: bio.tools is listed by: Debian is affiliated with: InterMOD is related to: AmiGO is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: HomoloGene is related to: TXTGate is related to: PhenoGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford University; Stanford; California is parent organization of: Ascomycete Phenotype Ontology is parent organization of: SGD Gene Ontology Slim Mapper is organization facet of: Alliance of Genome Resources |
NHGRI 5P41HG001315-11; NHGRI 5P41HG002273-05; NHGRI 5U41HG001315-18; NHGRI 2U41HG002273-13; NHGRI 5R01HG004834-04 |
PMID:24265222 PMID:12519985 PMID:9399804 |
Free for academic use, The community can contribute to this resource, Non-commercial | nif-0000-03456, biotools:sgd, r3d100010419, OMICS_01661 | https://bio.tools/sgd, https://doi.org/10.17616/R3N313 | http://genome-www.stanford.edu/Saccharomyces/ | SCR_004694 | SGD LOCUS, Saccharomyces Genome Database, SGD REF | 2026-07-25 12:11:31 | 1920 | |||
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Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators. | stem cell, facility, la jolla, pluripotent stem cells, ipsc, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014856 | SBP Medical Discovery Institute Stem Cell Core, SBP Stem Cell Core | 2026-07-25 12:13:02 | 0 | ||||||||||
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sleipner Resource Report Resource Website 1+ mentions |
sleipner (RRID:SCR_018143) | software resource, software toolkit | Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm. | Longitudinal data, analysis, cross sectional data, pattern oriented analysis, | has parent organization: Stockholm University; Stockholm; Sweden | Restricted | SCR_018143 | SLEIPNER, Sleipner, SLEIPNER 2.1 | 2026-07-25 12:13:03 | 2 | |||||||||
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meta Resource Report Resource Website 50+ mentions |
meta (RRID:SCR_019055) | software resource, software toolkit | Software general R package providing standard methods for meta analysis. | Meta analysis, standard methods, meta in R, analysis, statistics |
is listed by: CRAN is related to: dmetar has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
DOI:10.1007/978-3-319-21416-0 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/meta/meta.pdf | SCR_019055 | meta in R | 2026-07-25 12:13:04 | 61 | |||||||
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CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software resource, software toolkit | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | NSF DMS1763272; Simons Foundation ; NIH U01 AR073159; NIGMS R01 GM123731; NIH P30 AR07504; Pew Charitable Trust ; LEO Foundation ; UC Irvine ; Howard Hughes Medical Institute |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-07-25 12:13:07 | 536 | ||||||||
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ALEA Resource Report Resource Website 50+ mentions |
ALEA (RRID:SCR_006417) | ALEA | software resource, software toolkit | A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype. | allele, epigenomics, analysis, chip-seq, rna-seq, allelic variation, next-generation sequencing |
is listed by: OMICtools has parent organization: BC Cancer Agency |
PMID:24371156 | Academic Free License | OMICS_02193 | SCR_006417 | 2026-07-25 12:12:36 | 95 | |||||||
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Computational Genomics Analysis Tools Resource Report Resource Website 10+ mentions |
Computational Genomics Analysis Tools (RRID:SCR_006390) | CGAT | software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3, 2023. A collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome. | computational genomics, genomics, command-line, next-generation sequencing, python, pipeline, functional enrichment, clustering, metagenomic, contig, variant, analysis, filter, compare, conversion, summarization, annotation |
is listed by: OMICtools is related to: Galaxy has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:24395753 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02209 | SCR_006390 | Computational Genomics Analysis Toolkit, CGAT - Computational Genomics Analysis Tools | 2026-07-25 12:12:37 | 28 |
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