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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Blackfynn Discover Resource Report Resource Website 1+ mentions |
Blackfynn Discover (RRID:SCR_018068) | data or information resource, data repository, data set, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. Data repository for scientific data. Open data library to explore neuroscience data for neurodegenerative diseases for which there are no disease modifying treatments. | Neuroscience data, data repository, neurogenerative disease |
is used by: SPARC Portal is related to: Pennsieve Data Management Platform is organization facet of: SPARC Portal |
epilepsy, Parkinson, Alzheimer, neurodegenerative disease | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_018068 | SciCrunch Registry | 2026-09-26 02:16:03 | 1 | |||||||||
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BioSpherix: C-Chamber Resource Report Resource Website 1+ mentions |
BioSpherix: C-Chamber (RRID:SCR_018189) | instrument resource | Culture chamber for cell culture by BioSpherix. Functionalized by gas controllers for all bioactive gases, e.g. O2, CO2, CO, NO, etc. Made of clear polycarbonate. Magnetic seal door. Temperature is controlled. Combines with ProOx 110, ProCO2, ProOx C21, OxyCycler Series. | Culture chamber, cell culture, BioSpherix, incubator, gas controlled, temperature controlled, instrument, equipment | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018189.pdf | https://biospherix.com/wp-content/uploads/2017/11/Cell-Research-Literature_C-Chamber-Subchamber.pdf | SCR_018189 | SciCrunch Registry | C-Chamber, Culture Chamber | 2026-09-26 02:16:05 | 1 | ||||||||
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MaxTRAQ Resource Report Resource Website 1+ mentions |
MaxTRAQ (RRID:SCR_018188) | data analysis software, data processing software, software application, software resource | Software package for motion capture analysis by Innovision Systems Inc. | Motion capture, analysis, data, data tracking, Innovision Systems Inc. | Restricted | SCR_018188 | SciCrunch Registry | Innovision Systems MaxTRAQ software | 2026-09-26 02:16:05 | 2 | ||||||||||
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Sony biotechnology: SH800S Cell Sorter Resource Report Resource Website 10+ mentions |
Sony biotechnology: SH800S Cell Sorter (RRID:SCR_018066) | instrument resource | Benchtop cell sorter that sorts wide range of cell sizes for many applications using microfluidic sorting chips. Integrated with comprehensive fluidics controls and advanced automation for set-up, acquisition, sort and analysis. System software supports sorting into tubes and 96- and 384-well plates. Software generates FCS 3.0 and FCS 3.1 files that can be exported to third party analysis tools. For non-clinical research use only. For applications in which cross-contamination is concern, optional e-beam sterilized consumables can be used to replace sample line and sorting chip. Optional class A2 Level II biosafety cabinet provides protection for personnel and products. Biosafety cabinet meets international standards.Optical design offers up to four collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and six fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection. | ABRF, benchtop cell sorter, instrument, Sony Biotechnology, equipment | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018066.pdf | Model_Number_SH800S | https://www.sonybiotechnology.com/wordpress/wp-content/uploads/2016/05/Sony_SH800S.pdf | SCR_018066 | SciCrunch Registry | SH800 cell sorter | 2026-09-26 02:16:03 | 20 | |||||||
|
CRISPRdirect Resource Report Resource Website 500+ mentions |
CRISPRdirect (RRID:SCR_018186) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | SciCrunch Registry | 2026-09-26 02:16:05 | 588 | ||||||
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FoldIndex Resource Report Resource Website 1+ mentions |
FoldIndex (RRID:SCR_018390) | data access protocol, service resource, software resource, web service | Web tool to predict whether given protein sequence is intrinsically unfolded. Algorithm for predicting ordered and disordered regions in protein based on its primary structure amino acid sequence. Graphic web server to predict if given protein sequence is intrinsically unfolded implementing algorithm of Uversky and co-workers, which is based on average residue hydrophobicity and net charge of sequence. | Protein sequence, intrinsically unfolded sequence, protein ordered region, protein disordered region, amino acid structure, protein region prediction | Divadol Foundation ; Israel Ministry of Science and Technology ; Minerva Foundation |
DOI:10.1093/bioinformatics/bti537 | Free, Freely available | SCR_018390 | SciCrunch Registry | 2026-09-26 02:16:07 | 4 | |||||||||
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NBRP Medaka Pattern Match Resource Report Resource Website 1+ mentions |
NBRP Medaka Pattern Match (RRID:SCR_018157) | analysis service resource, data or information resource, database, production service resource, service resource | Web medaka pattern match tool for short sequence and/or pattern. Used to search database of medaka genome on target and off target sites when editing genome with CRISRP-Cas9. | Medaka, pattern match tool, short sequence, pattern, medaka genome, target site, off target site, editing genome, CRISP-Cas9 | has parent organization: Kyoto University; Kyoto; Japan | Free, Freely available | SCR_018157 | SciCrunch Registry | 2026-09-26 02:16:04 | 5 | ||||||||||
|
O Resource Report Resource Website 1+ mentions |
O (RRID:SCR_018394) | 3d spatial image, 3d visualization software, data or information resource, data processing software, data visualization software, image, software application, software resource | Software for visualization of macromolecular structures, atomic coordinates, and 3D intensity maps, and for building macromolecular structures. | Macromolecular structure, atomic coordinate, protein structure, 3D visualization, model building, atomic modelling | has parent organization: Uppsala University; Uppsala; Sweden | DOI:10.1107/s0108767390010224 | Free, Available for download, Freely available | SCR_018394 | SciCrunch Registry | 2026-09-26 02:16:07 | 1 | |||||||||
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Mizar Imaging: Tilt High Resolution Light Sheet Imaging System Resource Report Resource Website |
Mizar Imaging: Tilt High Resolution Light Sheet Imaging System (RRID:SCR_018156) | instrument resource | Modular light sheet illumination system designed to image living samples with minimal photobleaching or phototoxicity by Mizar Imaging. Enables high spatial and temporal resolution light sheet imaging to be added to existing or new microscope system. | Mizar Imaging, light sheet imaging, modular homology, illumination system, image living sample, minimal photobleaching, minimal phototoxicity, microscope system, instrument, equipment | Restricted | https://www.mizarimaging.com/wp-content/uploads/2018/11/Tilt-Datasheet-3.pdf | SCR_018156 | SciCrunch Registry | Tilt | 2026-09-26 02:16:04 | 0 | |||||||||
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COVID-19 research data on Figshare Resource Report Resource Website |
COVID-19 research data on Figshare (RRID:SCR_018277) | data or information resource, portal, topical portal | Portal to discover COVID-19 open research data on Figshare. Figshare collection of COVID-19 related research data. | COVID-19, COVID-19 data, open research data | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018277 | SciCrunch Registry | 2026-09-26 02:16:06 | 0 | |||||||||
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S2 Genomics: Singulator 100 Automated Single Cell Prep Automated System Resource Report Resource Website 1+ mentions |
S2 Genomics: Singulator 100 Automated Single Cell Prep Automated System (RRID:SCR_018155) | instrument resource | Singulator to automate tissue preparation for single cell and single nucleus analyses. Bench top Singulator System and single use cartridge enable tissue dissociations into singulated cells or nuclei suspensions. | S2 Genomics, automated cell preparation, tissue preparation, single cell, single nucleus analysis, benchtop, singulator system, single use cartridge, singulated cell suspension, singulated nuclei suspension, instrument, equipment | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018155.pdf | https://s2genomics.com/wp-content/uploads/2022/08/S2-Genomics-Singulator-100-Brochure-v220804.pdf | SCR_018155 | SciCrunch Registry | S2 Genomics Singulator, S2 Genomics Singulator 100, Singulator 100 | 2026-09-26 02:16:04 | 2 | ||||||||
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MS Amanda Resource Report Resource Website 1+ mentions |
MS Amanda (RRID:SCR_018396) | algorithm resource, data analysis software, data processing software, software application, software resource | Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria. | Tandem mass spectrometry, protein database, scoring system, peptide identification, data, search algorithm, protein identification algorithm, peptide identification, proteomic | is related to: PeptideShaker | Austrian Science Fund ; European Community Seventh Framework Programme ; MeioSys |
PMID:24909410 | Free, Available for download, Freely available | https://ms.imp.ac.at/?goto=msamanda | SCR_018396 | SciCrunch Registry | MS Amanda 2.0, Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra | 2026-09-26 02:16:07 | 2 | ||||||
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Black Zen software Resource Report Resource Website 100+ mentions |
Black Zen software (RRID:SCR_018163) | data processing software, image analysis software, image processing software, software application, software resource | Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments. | Free, Available for download, Freely available | http://microscopy.arizona.edu/sites/default/files/sites/default/files/upload/Installing%20the%20free%20Zeiss%20ZEN%20software%20on%20a%20Windows%20PC%20%28rev2018%29.pdf | SCR_018163 | SciCrunch Registry | ZEISS ZEN Microscope Software, Black Zen software (ZEISS), ZEN Black | 2026-09-26 02:16:04 | 169 | ||||||||||
|
outbreak.info Resource Report Resource Website 100+ mentions |
outbreak.info (RRID:SCR_018282) | data or information resource, portal, topical portal | Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19. | COVID-19 data collection, single location, outbreak information, emerging disease |
is listed by: Data and Computational Resources to Address COVID-19 has parent organization: Scripps Research Institute |
COVID-19 | NIAID | Free, Freely available | SCR_018282 | SciCrunch Registry | 2026-09-26 02:16:06 | 155 | ||||||||
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Data-Against-COVID Team Resource Report Resource Website |
Data-Against-COVID Team (RRID:SCR_018288) | data or information resource, portal, topical portal | Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic. | Data scientist, volunteer, machine learning expert, bioinformaticians, professional software developer, data analysis, coronavirus pandemic | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018288 | SciCrunch Registry | 2026-09-26 02:16:06 | 0 | |||||||||
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Cloud resources for COVID-19 research Resource Report Resource Website |
Cloud resources for COVID-19 research (RRID:SCR_018286) | data or information resource, portal, topical portal | Cloud resources for COVID-19 research provided by Rescale, Google Cloud, and Microsoft Azure. High performance computing resources immediately available for COVID-19 research. | Cloud resorce, COVID-19, Rescale, Google Cloud, Microsoft Azure, computing resource | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018286 | SciCrunch Registry | 2026-09-26 02:16:06 | 0 | |||||||||
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NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource, topical portal | Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools. | Visualization, analysis, multi omic data, cell type, developing brain, adult brain, RNAseq, ATACseq, CHIPseq, fetal human prefrontal cortex, stem cell, neural induction, brain, data |
is used by: BICCN is related to: NeMOarchive is related to: BRAIN Initiative is related to: Brainome portal is related to: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_018244 | SCR_018164 | SciCrunch Registry | Neuroscience Multi-Omic Analytics | 2026-09-26 02:16:04 | 16 | ||||||||
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Eppendorf: 5920R centrifuge Resource Report Resource Website 1+ mentions |
Eppendorf: 5920R centrifuge (RRID:SCR_018092) | instrument resource | Swinging bucket benchtop centrifuge. Eppendorf 5920 R refrigerated centrifuge. | Centrifuge, swinging bucket, benchtop, Eppendorf, refrigerated centrifuge, instrument, equipment | Restricted | https://www.eppendorf.com/product-media/doc/en/330744/Centrifugation_Operating-manual_Centrifuge-5920-R.pdf | SCR_018092 | SciCrunch Registry | 2026-09-26 02:16:04 | 1 | ||||||||||
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Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | data processing software, software application, software resource, workflow software | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Key Research and Development Program 2017YFC0908500 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 81573023 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | SciCrunch Registry | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-09-26 02:16:05 | 2 | |||||
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Precisionary: Compresstome VF-700 Resource Report Resource Website 1+ mentions |
Precisionary: Compresstome VF-700 (RRID:SCR_018409) | instrument resource | Vibrotome by Precisionary Instruments designed for cutting fixed tissue slices for histology studies. Offers two point stabilization of blade holder to eliminate unwanted chatter marks on surfaces of tissue slice. Fully automated to section fixed tissues with thickness range of 4 um to 2000 um with adjustable precision of 1 um. | Precisionary Instrument, cutting fixed tissue, tissue slice, histology, two point stabilization blade holder, instrument, equipment | Restricted | https://nbtltd.com/wp-content/uploads/2019/11/compresstome-vf-700-0z-user-manual_final.pdf | SCR_018409 | SciCrunch Registry | Compresstome VF-700-0Z | 2026-09-26 02:16:07 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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