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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Intensity Ratio Nuclei Cytoplasm Tool Resource Report Resource Website 10+ mentions |
Intensity Ratio Nuclei Cytoplasm Tool (RRID:SCR_018573) | image analysis software, software application, software resource, data processing software, image processing software | Software tool to calculate ratio of intensity in nuclei and cytoplasm. It needs two images as input cytoplasm channel and nuclei channel. | Intensity ratio, nuclei, cytoplasm, image, cytoplasm channel, nuclei channel, calculate ration, ImageJ | works with: ImageJ | Free, Freely available | SCR_018573 | 2026-08-01 12:06:00 | 35 | ||||||||||
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Custom made 30 kDa microdialysis probe Resource Report Resource Website 1+ mentions |
Custom made 30 kDa microdialysis probe (RRID:SCR_018571) | instrument resource | Probe uses semi permeable membrane with pore size of 30 kDa which enables small hydrophilic compounds from brain extracellular space to diffuse passively into perfusate. Used to measure extracellular ACh level and glucose metabolites directly without purification. | PMID:25172804 | Restricted | SCR_018571 | 2026-08-01 12:06:15 | 1 | |||||||||||
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BioVelocity Resource Report Resource Website 1+ mentions |
BioVelocity (RRID:SCR_018501) | image analysis software, data analysis software, alignment software, software application, software resource, sequence analysis software, data processing software | Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes. | Hashing algorithm, genomic reference indices, Noblis, indexing genomic reference, align reads, reference genome, random position, k-mer index, index match reference genome | Restricted | SCR_018501 | 2026-08-01 12:06:21 | 1 | |||||||||||
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Luminex: Amnis ImageStreamX Mk II System Resource Report Resource Website 100+ mentions |
Luminex: Amnis ImageStreamX Mk II System (RRID:SCR_018589) | instrument resource | Bench top multispectral imaging flow cytometer designed for the acquisition of up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry. | Benchtop Flow Cytometer, Instrument, Equipment, imaging flow cytometer, USEDit, Luminex | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018589.pdf | SCR_020244, SCR_020142, Model_Number_ImageStreamX_MkII | https://www.unthsc.edu/research/wp-content/uploads/sites/21/AMNIS-Imagestream.pdf | https://www.luminexcorp.com/imagestreamx-mk-ii/ | SCR_018589 | , Luminex ImageStream MkII Multispectral Imaging Flow Cytometer, MkII imaging flow cytometer, Luminex ImageStream MkII Flow Cytometer, Luminex Amnis ImageStream MkII Multispectral Imaging Flow Cytometer | 2026-08-01 12:06:15 | 130 | |||||
|
ReproNim/containers Resource Report Resource Website 1+ mentions |
ReproNim/containers (RRID:SCR_018467) | knowledge environment resource, data or information resource, software toolkit, portal, workflow, narrative resource, software resource, training material | Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments. | Containerized environment, reproducible neuroimaging, ReproNim, neuroimaging, dataset, DataLad, imaging, data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIBIB P41 EB019936; NSF 1429999; German Federal Ministry of Education and Research |
Free, Freely available | https://github.com/ReproNim/containers | SCR_018467 | 2026-08-01 12:06:14 | 1 | ||||||||
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Codon Usage Analyzer Resource Report Resource Website |
Codon Usage Analyzer (RRID:SCR_018500) | Bio::CUA, Bio-CUA | data processing software, data analysis software, software application, software resource | Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems. | Codon usage analyzer, codon, codon usage bias, genome, gene, codon, sequence | has parent organization: University of Rochester; New York; USA | David and Lucile Packard Foundation ; University of Rochester |
DOI:10.1101/022814 | Free, Freely available | https://metacpan.org/release/Bio-CUA | SCR_018500 | 2026-08-01 12:06:14 | 0 | ||||||
|
SpoTyping Resource Report Resource Website 10+ mentions |
SpoTyping (RRID:SCR_018466) | data processing software, data analysis software, software application, software resource | Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads. | bio.tools |
is listed by: bio.tools is listed by: Debian |
National University of Singapore ; Singapore ; Singapore |
DOI:10.1186/s13073-016-0270-7 | Free, Available for download, Freely available | biotools:spotyping | https://bio.tools/spotyping | SCR_018466 | SpoTyping-v2.0, SpoTyping | 2026-08-01 12:06:21 | 10 | |||||
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BisoGenet Resource Report Resource Website 1+ mentions |
BisoGenet (RRID:SCR_018502) | data visualization software, software toolkit, data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18, 2020. Software package to create, visualize and analyze biological networks. Can include coding relations to distinguish between genes and their products. BisoGenet client is designed to work as Cytoscape plugin for querying server along with graph topology analysis and visualization options for easing interpretation process. | Center for Genetic Engineering and Biotechnology from Havana ; Cuba. ; INSPUR Electronic Information Industry ; Beijing |
PMID:20163717 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018502 | 2026-08-01 12:06:14 | 4 | ||||||||||
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Campden Instruments: Vibroslice vibrating microtome Resource Report Resource Website 1+ mentions |
Campden Instruments: Vibroslice vibrating microtome (RRID:SCR_018460) | instrument resource | Vibrating microtome manufactured by Campden Instruments. 752 Vibroslice tissue cutter for manual tissue transport. | vibratome, vibrating microtome, Campden Instruments Inc., Vibroslice | Restricted | https://www.limef.com/Downloads/752-752M%20manual.pdf | SCR_018460 | 752 vibroslice tissue cutter | 2026-08-01 12:06:21 | 3 | |||||||||
|
Fujifilm: FLA-5100 Scanner Resource Report Resource Website |
Fujifilm: FLA-5100 Scanner (RRID:SCR_018581) | instrument resource | EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method. | Scanner, Instrument, Equipment, ABRF | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018581.pdf | Model_Number_FLA_1500, SCR_019925 | http://www.raytek.co.uk/Brochures/FLA5100%20UK-IE%20Brochure.pdf | SCR_018581 | 2026-08-01 12:06:15 | 0 | |||||||||
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Illumina: cBot Genetic Amplifier Resource Report Resource Website 1+ mentions |
Illumina: cBot Genetic Amplifier (RRID:SCR_018580) | instrument resource | Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures. | Illumina, Genetic Amplifier, Instrument Equipment, USEDit | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018580.pdf | SCR_020129, Model_Number_cBot | https://www.illumina.com/documents/products/datasheets/datasheet_cbot.pdf | https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/cbot/cbot-system-guide-15006165-04.pdf | SCR_018580 | 2026-08-01 12:06:22 | 1 | ||||||
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Kent Scientific: Coda Blood Pressure System Resource Report Resource Website 10+ mentions |
Kent Scientific: Coda Blood Pressure System (RRID:SCR_018585) | instrument resource | CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. Using the included software allows you to continuously view data in real-time. | Blood Pressure System, Instrument, Equipment, Mouse Blood Pressure Measuring Equipment, USEDit, Kent Scientific | is listed by: USEDit | Restricted | https://www.kentscientific.com/Customer-Content/www/products/Files/CODA_High_Thrpt_Manual_V2_00_02.pdf | SCR_018585 | 2026-08-01 12:06:22 | 13 | |||||||||
|
LASTZ Resource Report Resource Website 10+ mentions |
LASTZ (RRID:SCR_018556) | image analysis software, software toolkit, alignment software, software application, data processing software, software resource | Software package for sequence alignment. Pairwise aligner for aligning DNA sequences. Designed to handle sequences size of human chromosomes and from different species. Useful for sequences produced by NGS sequencing technologies. | Sequence, sequence alignment, pairwise aligner, DNA sequence alingning, human chromosome, Next Generation Sequencing technology data | has parent organization: Miller Lab at the Penn State Center for Comparative Genomics and Bioinformatics | Free, Available for download, Freely available | http://www.bx.psu.edu/~rsharris/lastz/, https://github.com/lastz/lastz | SCR_018556 | 2026-08-01 12:06:15 | 39 | |||||||||
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Agilent: 3100 OFFGEL Fractionator Resource Report Resource Website 1+ mentions |
Agilent: 3100 OFFGEL Fractionator (RRID:SCR_018433) | instrument resource | Agilent 3100 OFFGEL Fractionator performs isoelectric focusing of proteins or peptides in immobilized pH gradient (IPG) gel strips. | Fractionator, Instrument, Equipment, Electrophoresis, Agilent, USEDit, ABRF, | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018433.pdf | SCR_018442, SCR_019388 | https://www.agilent.com/Library/usermanuals/Public/G3100-90001_OFFGEL_UserManual_ebook.pdf | SCR_018433 | Agilent 3100 OFFGEL Fractionator | 2026-08-01 12:06:20 | 1 | |||||||
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Thermo Fisher: Applied Biosystems: ABI Voyager DE Pro MALDI-Mass Spectrometer Resource Report Resource Website |
Thermo Fisher: Applied Biosystems: ABI Voyager DE Pro MALDI-Mass Spectrometer (RRID:SCR_018432) | instrument resource | Benchtop MALDI TOF mass spectrometer that has linear and reflector analyzer. It is used to analyze organic and inorganic compounds, protein identification, synthetic peptide validation, and polymer analysis. | Benchtop Mass Spectrometer, MALDI TOF, Instrument, Equipment, ABI, MALDI, ABRF, USEDit | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018432.pdf | , SCR_018445 | https://tools.thermofisher.com/content/sfs/brochures/cms_039956.pdf | SCR_018432 | 2026-08-01 12:05:58 | 0 | ||||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | image analysis software, alignment software, software application, software resource, data processing software | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | 2026-08-01 12:06:21 | 1325 | ||||||
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Nanotomy Resource Report Resource Website 10+ mentions |
Nanotomy (RRID:SCR_018565) | data or information resource, data repository, storage service resource, database, service resource, data set, image collection | Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes. | Large scale, electron microscopy, data set, Human Type 1 Diabetes, image collection |
is related to: Golddigger has parent organization: University of Groningen; Groningen; Netherlands |
Type 1 diabetes, Diabetes | PMID:32424134 | Free, Freely available | SCR_020961 | SCR_018565 | nano-anatomy, Anatomy at nanoscale, nanotomy | 2026-08-01 12:06:15 | 25 | ||||||
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TimeZone Resource Report Resource Website 1+ mentions |
TimeZone (RRID:SCR_018564) | data processing software, data analysis software, software application, software resource | Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes. | Detect footprint, positive selection, functionally adaptive, point mutation, microbial genome | NIGMS R01 GM084318; NIAID RC4 AI092828 |
PMID:23471110 | Free, Available for download, Freely available | SCR_018564 | 2026-08-01 12:06:21 | 1 | |||||||||
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Doric Neuroscience Studio Resource Report Resource Website 10+ mentions |
Doric Neuroscience Studio (RRID:SCR_018569) | data acquisition software, software application, data processing software, software resource | Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected. | Doric, Doric hardware control, data acquire | Restricted | SCR_018569 | 2026-08-01 12:06:00 | 19 | |||||||||||
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ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data visualization software, software application, data processing software, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-08-01 12:06:21 | 54 |
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