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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | data analysis software, data processing software, software application, software resource, software toolkit | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NHGRI P50 HG006193; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NIH Office of the Director DP2 OD00667; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2026-09-12 12:59:04 | 342 | ||||||
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Nikon: AZ100 Confocal Microscope Resource Report Resource Website 1+ mentions |
Nikon: AZ100 Confocal Microscope (RRID:SCR_018603) | instrument resource | Nikon Instruments AZ100 C1si is macro confocal microscope system combining stereo and compound microscopes into single hybrid imaging system for dynamic imaging of single cells or whole specimens.System covers range of magnifications from 5x to 400x. Has triple nosepiece that can switch magnifications. AZ100 C1si boasts simultaneous 32 channel spectral image acquisition over spectral range of 320 nm in single scan. Simultaneous 32 channel acquisition at 10 nm, 5 nm or 2.5 nm bandwidths, all software controlled, is possible. | Confocal Microscope, Instrument, Equipment, Nikon, USEDit, ABRF | is listed by: USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018603.pdf | Model_Number_AZ100, SCR_020325 | https://www.mvi-inc.com/wp-content/uploads/AZ100-Manual.pdf | SCR_018603 | 2026-09-12 12:59:03 | 2 | |||||||
|
MicroFilePlus Resource Report Resource Website 1+ mentions |
MicroFilePlus (RRID:SCR_018724) | data processing software, image processing software, software application, software resource | Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources. | Image file format, image converter, converter, OME-TIFF Format, jpeg2000, jpx, JP2, MBF Bioscience | Restricted | SCR_018724 | MicroFilePlus, MicroFile+, microfileplus | 2026-09-12 12:59:05 | 2 | ||||||||||
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Marshall Scientific: MJ Research PTC-100 PCR Thermocycler Resource Report Resource Website 10+ mentions |
Marshall Scientific: MJ Research PTC-100 PCR Thermocycler (RRID:SCR_018602) | instrument resource | Thermocycler that operates with 96 well and 60 well microplates. Has temperature configurations from 0 C to 105 C and pressure and height adjustment via thumbwheel. Comes with 14 pre-programmed protocols. | PCR Thermocycler, Instrument, Equipment, USEDit, MJ Research, ABRF | is listed by: USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018602.pdf | Model_Number_PTC100, SCR_020292 | https://www.artisantg.com/info/MJ_PTC_100_Manual.pdf | SCR_018602 | 2026-09-12 12:59:03 | 12 | |||||||
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Waters: 2695 HPLC System Resource Report Resource Website 1+ mentions |
Waters: 2695 HPLC System (RRID:SCR_018649) | instrument resource | High performance liquid chromatographic system with quaternary, low pressure mixing pump and inline vacuum degassing. It has wavelengths of 190 to 800 nm and flow rates from 50 uL per min to 5 mL per min with 2.1 mm ID columns and larger. Autosampler has maximum capacity of 120 vials (12x32, 2 mL) with programmable temperature control from 4 to 40C. Heated column compartment provides temperatures from 5 degrees above ambient to 65C. | HPLC System, Instrument, Equipment, USEDit, Waters, ABRF | is listed by: USEDit | Commercially available | Model_Number_2695, SCR_020877 | https://www.waters.com/webassets/cms/library/docs/720004547en.pdf | SCR_018649 | Waters Alliance 2695 Separations Module | 2026-09-12 12:59:04 | 1 | |||||||
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BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, software resource, software toolkit, web service | Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. | Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools |
uses: BcForms is used by: ObjTables is used by: Datanator is listed by: Debian is listed by: bio.tools is related to: BcForms is related to: ObjTables |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | 2026-09-12 12:59:04 | 0 | ||||||
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ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data management software, data processing software, software application, software resource, software toolkit | Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. | Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools |
uses: BpForms uses: BcForms is listed by: bio.tools is listed by: Debian is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | 2026-09-12 12:59:04 | 0 | |||||||
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trend Resource Report Resource Website 1+ mentions |
trend (RRID:SCR_018658) | data analysis software, data processing software, software application, software resource, software toolkit | Software package includes tests for trends and change points detection. Used in analysis of environmental data. | tests for trend detection, environmental data analysis, Cox-Stuart Trend Test, Mann-Kendall Trend Test, Hirsch-Slack Test, partial Pearson and Spearman correlation trend test, change-point detection | is related to: CRAN | Free, Freely available | SCR_018658 | Non-Parametric Trend Tests and Change-Point Detection | 2026-09-12 12:59:04 | 1 | |||||||||
|
McKinley: Cellometer Auto 2000 Cell Viability Counter Resource Report Resource Website 1+ mentions |
McKinley: Cellometer Auto 2000 Cell Viability Counter (RRID:SCR_018656) | instrument resource | Cell viability counter. Touchscreen fluorescent automated cell counter for primary samples by Nexcelom Bioscience. | Cell viability counter, touchscreen cell counter, fluorescent automated cell counter, Nexcelom Bioscience, instrument, equipment | is related to: USEDit | Restricted | https://biotech.gsu.edu/core/Documents/Manuals/Cellometer2000.pdf | SCR_018656 | 2026-09-12 12:59:04 | 3 | |||||||||
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QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-09-12 12:59:04 | 27 | ||||||||
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Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | 2026-09-12 12:59:04 | 21 | |||||||
|
Thermo Fisher: QE-HFX mass spectrometer Resource Report Resource Website 10+ mentions |
Thermo Fisher: QE-HFX mass spectrometer (RRID:SCR_018703) | instrument resource | HFX offers scanning rate to improve proteomic depth for discovery applications. Integrates well with targeted applications such as parallel reaction monitoring. Mass Spectrometer to identify and quantify proteins, peptides, lipids, glycans and small molecules accurately. | Thermo Scientific, Mass Spectrometer, small molecules identification, small molecules quantification, Instrument, Equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018703.pdf | Model_Number_QE-HFX | https://assets.thermofisher.com/TFS-Assets/CMD/Specification-Sheets/PS-64048-LC-MS-Q-Exactive-HF-Orbitrap-PS64048-EN.pdf | https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFALGMBFZ#/IQLAAEGAAPFALGMBFZ | SCR_018703 | Thermo QE-HFX, Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer | 2026-09-12 12:59:04 | 11 | ||||||
|
Thermo Fisher: Orbitrap Fusion nanoLC/MS system Resource Report Resource Website 1+ mentions |
Thermo Fisher: Orbitrap Fusion nanoLC/MS system (RRID:SCR_018702) | instrument resource | System includes Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments. | Thermo Orbitrap Fusion Tribrid mass spectrometer, Waters M-Class Acquity nanoUPLC, instrument, equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://tools.thermofisher.com/content/sfs/brochures/PS-63844-LC-MS-Orbitrap-Fusion-PS63844-EN.pdf | SCR_018702 | Thermo Orbitrap Fusion nanoLC/MS, Orbitrap Fusion nanoLC/MS | 2026-09-12 12:59:04 | 4 | |||||||||
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Thermo Fisher: LTQ XL LC/MS system Resource Report Resource Website |
Thermo Fisher: LTQ XL LC/MS system (RRID:SCR_018701) | instrument resource | LTQ XL ion trap mass spectrometer with Agilent 1100 HPLC system for metabolite identification, stability testing, degradation products, and high abundance quantitation. | LTQ XL ion trap, mass spectrometer, Agilent 1100 HPLC, metabolite identification, stability testing, degradation product, high abundance quantitation, equipment, instrument, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://www.pragolab.cz/documents/LTQ_XL_PS1.pdf | SCR_018701 | Thermo LTQ XL LC/MS | 2026-09-12 12:59:04 | 0 | |||||||||
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Discrete Morse Resource Report Resource Website |
Discrete Morse (RRID:SCR_018662) | DM | data processing software, image processing software, software application, software resource | Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections. | Neuron tracing, tracer injection, single neuron data set, set of trees summarization generation, neuron image data, extract individual neuron tree skeleton, volumetric brain image data, summarize collection, tracer injection labelled neuron | DOI:10.1101/2020.03.21.000323v1 | Free, Freely available | SCR_018662 | DiscreteMorse | 2026-09-12 12:59:04 | 0 | ||||||||
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minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data analysis software, data processing software, network analysis software, software application, software resource, software toolkit | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-09-12 12:59:04 | 0 | |||||
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MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, service resource, software resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCATS UL1 TR001114; NCI K22 CA188163; NHGRI U01 HG006476; NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info, https://bio.tools/mygene.info, https://bio.tools/mygene.info | SCR_018660 | 2026-09-12 12:59:04 | 34 | ||||||
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Stratagene: 1800 UV Crosslinker Resource Report Resource Website |
Stratagene: 1800 UV Crosslinker (RRID:SCR_018631) | instrument resource | UV crosslinker designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon reinforced nitrocellulose membranes in 25 to 50 seconds. It is equipped with internal photodetector to compensate for aging ultraviolet bulbs. | Crosslinker, Instrument, Equipment, USEDit, ABRF, Stratagene | is listed by: USEDit | Commercially available | Model_Number_1800, SCR_020532 | https://ipmb.sinica.edu.tw/microarray/index.files/Stratalinker%20UV%20Crosslinker.pdf | SCR_018631 | 2026-09-12 12:59:03 | 0 | ||||||||
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SCIEX: 4000 QTRAP Mass Spectrometer Resource Report Resource Website |
SCIEX: 4000 QTRAP Mass Spectrometer (RRID:SCR_018630) | instrument resource | Hybrid triple quadrupole linear ion trap mass spectrometer for drug discovery and development, metabolite identification, contaminant testing, proteomic applications, post translationally modified proteins discovery, protein identification, and biomarker validation. | Mass Spectrometer, Instrument, Equipment, USEDit, Sciex, ABRF | is listed by: USEDit | Commercially available | SCR_020508, Model_Number_Sciex_4000_QTRAP | https://collateral.sciex.com/manuals/4000-qtrap-hardware-guide/4000-qtrap-hardware-guide.pdf | SCR_018630 | 2026-09-12 12:59:03 | 0 | ||||||||
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TA Instruments: Electroforce 3200 Mechanical Testing Apparatus Resource Report Resource Website 1+ mentions |
TA Instruments: Electroforce 3200 Mechanical Testing Apparatus (RRID:SCR_018637) | instrument resource | Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications.. | Mechanical Testing Apparatus, Instrument, Equipment, USEDit, ABRF | is listed by: USEDit | SCR_019752, Model_Number_3200 | https://www.tainstruments.com/wp-content/uploads/ElectroForce_Test_Instruments.pdf | SCR_018637 | TA Instruments Electroforce 3200 Series Mechanical Testing Apparatus | 2026-09-12 12:59:04 | 2 |
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