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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Zeiss: Auriga Auriga Resource Report Resource Website |
Zeiss: Auriga Auriga (RRID:SCR_020914) | instrument resource | Electron microscope with pulsed laser beam that creates images in high resolution in the nanometre range. This miscroscope allows the user to investigate your samples with X-ray analysis, rework interesting sample positions, and analyze non-conducting material and complex geometries. | Generic | Commercially available | Model_Number_Auriga | SCR_020914 | SciCrunch Registry | 2026-10-10 12:41:19 | 0 | ||||||||||
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PAM Resource Report Resource Website 1+ mentions |
PAM (RRID:SCR_020966) | data analysis software, data processing software, software application, software resource | Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities. | Quantitative data analysis, fluorescence microscopy data, data analysis, spectroscopy data analysis, pulsed interleaved excitation, imaging integrated analysis |
uses: MATLAB has parent organization: Ludwig-Maximilians-University; Munich; Germany |
Deutsche Forschungsgemeinschaft ; Ludwig-Maximilians-University; Munich; Germany ; Research Foundation Flanders |
PMID:29642023 | Free, Available for download, Freely available | http://www.cup.uni-muenchen.de/pc/lamb/software/pam.html | SCR_020966 | SciCrunch Registry | Pulsed interleaved excitation Analysis with Matlab, Pulsed Interleaved Excitation analysis with MATLAB, PIE analysis with MATLAB | 2026-10-10 12:41:23 | 4 | ||||||
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Olympus: LEXT OLS4100 laser confocal microscope Resource Report Resource Website |
Olympus: LEXT OLS4100 laser confocal microscope (RRID:SCR_020969) | instrument resource | Laser scanning digital microscope for non-contact 3D observations and measurements of surface features at 10 nanometer resolutions with fast image acquisition and high-resolution images over wider area. Z-drive moves in steps less than 1nm, accuracy and repeatability guaranteed by Olympus. The system includes 5 objectives: 5x/0.15, 10x/0.30, 20x/0.60, 50x/0.95, and 100x/0.95. | surface metrology, laser scanning, digital microscope, non-contact 3D observations, Olympus | Discontinued | SCR_020969 | SciCrunch Registry | 2026-10-10 12:41:20 | 0 | |||||||||||
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Beckman Research Institute of City of Hope Resource Report Resource Website |
Beckman Research Institute of City of Hope (RRID:SCR_020975) | institution | Not-for-profit medical research facility located at and partnering with the City of Hope National Medical Center in Duarte, CA, United States.Fields of research include Cancer, Diabetes, Metabolic disorder, HIV/AIDS. | SCR_020975 | SciCrunch Registry | 2026-10-10 12:41:23 | 0 | |||||||||||||
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Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | data analysis software, data processing software, software application, software resource | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | SciCrunch Registry | Flowlogic TM Software, Flowlogic Software | 2026-10-10 12:41:14 | 81 | |||||||||
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Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels. | Versatile aligning pipeline, bisulfite sequencing data, mapping bisulfite sequencing data, generating DNA methylomes, DNA methylation level, reads mapping, Reduced Represented Bisulfite Sequencing library, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: BS Seeker has parent organization: University of California at Los Angeles; California; USA |
China Scholarship Council ; Institute of Genomics and Proteomics at UCLA ; NBRPC 2012CB316503 |
PMID:24206606 | Free, Available for download, Freely available | biotools:bs-seeker2 | http://pellegrini.mcdb.ucla.edu/BS_Seeker2/, https://bio.tools/bs-seeker2 | SCR_020948 | SciCrunch Registry | Bisulfite Sequencing Seeker2, BS Seeker2 | 2026-10-10 12:41:14 | 2 | |||||
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MITE-Hunter Resource Report Resource Website 1+ mentions |
MITE-Hunter (RRID:SCR_020946) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences. | Class 2 non-autonomous transposable element, genes non-coding regions, genome evolution, coding sequence, genomic DNA data sets, | NSF 0607123 | PMID:20880995 | Free, Available for download, Freely available | https://github.com/jburnette/MITE-Hunter | SCR_020946 | SciCrunch Registry | Miniature Inverted repeat Transposable Elements Hunter | 2026-10-10 12:41:43 | 7 | |||||||
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cgmapotools Resource Report Resource Website 1+ mentions |
cgmapotools (RRID:SCR_020950) | data analysis software, data processing software, software application, software resource | Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. | DNA methylomes analysis, DNA methylomes, context-wise analysis, gene-wise analysis, bin-wise analysis, region-wise analysis, sample-wise analysis, bisulfite sequencing data, allele specific methylation detection | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:28968643 | Free, Available for download, Freely available | SCR_020950 | SciCrunch Registry | 2026-10-10 12:41:20 | 3 | |||||||||
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Hugging Face Resource Report Resource Website 100+ mentions |
Hugging Face (RRID:SCR_020958) | community building portal, data or information resource, organization portal, portal | Portal to build, train and deploy state of the art models powered by reference open source in natural language processing. | Hugging Face, Inc., NLP, Natural Language Processing, build art models, deploy art models, reference open source | Free, Freely available | https://github.com/huggingface | SCR_020958 | SciCrunch Registry | 2026-10-10 12:41:20 | 121 | ||||||||||
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MesKit Resource Report Resource Website 1+ mentions |
MesKit (RRID:SCR_020959) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, software toolkit | Software R package for dissecting cancer evolution from multi region derived tumor biopsies via somatic mutations. Used for characterizing cancer genomic ITH and inferring history of tumor evolution via implementation of well established computational and statistical methods. | Dissecting cancer evolution, region derived tumor biopsies, somatic mutations, cancer genomic ITH, tumor evolution | has parent organization: Sun Yat-sen University; Guangdong; China | Free, Available for download, Freely available | https://bioconductor.org/packages/MesKit/ | SCR_020959 | SciCrunch Registry | Multi region exome sequencing analysis tool Kit | 2026-10-10 12:41:43 | 4 | ||||||||
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Perkin Elmer: Opera Phenix Plus High Content Screening System Resource Report Resource Website 10+ mentions |
Perkin Elmer: Opera Phenix Plus High Content Screening System (RRID:SCR_021100) | instrument resource | Opera Phenix Plus system for high throughput high content assays, phenotypic screening, assays using complex disease models, such as live cells, primary cells and microtissues, and fast response assays like calcium flux or cardiomyocyte beating.Optical design lets you generate information through confocal imaging and at higher throughput through simultaneous acquisition. Delivers speed without compromising sensitivity. Uses Harmony High Content Imaging and Analysis Software to quantify complex cellular phenotypes. Harmony software is designed for PerkinElmer high content screening systems. | PerkinElmer, confocal imaging, simultaneous acquisition, high throughput high content assays, phenotypic screening, Harmony software, high content screening systems, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021100.pdf | Model_Number_Opera_Phenix_Plus | https://www.perkinelmer.com/Product/opera-phenix-plus-system-hh14001000 | SCR_021100 | SciCrunch Registry | Opera Phenix Plus | 2026-10-10 12:41:46 | 14 | |||||||
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Nikon: ECLIPSE Ti2 inverted microscope Resource Report Resource Website 10+ mentions |
Nikon: ECLIPSE Ti2 inverted microscope (RRID:SCR_021068) | instrument resource | Inverted microscope delivers unparalleled 25mm field of view. With this FOV, the Ti2 maximizes sensor area of large format CMOS cameras without making compromises, and significantly improves data throughput. Stable, drift free platform designed to meet demands of super resolution imaging with high speed imaging applications. Status of each sensor is automatically recorded during acquisition, providing quality control for imaging experiments and enhancing data reproducibility. | Nikon, inverted microscope, Instrument, Equipment, USEDit |
is related to: Nikon: ECLIPSE Ti inverted microscope system works with: NIS-Elements |
Commercially available | Model_Number_Ti2 | SCR_021068 | SciCrunch Registry | ECLIPSE Ti2, Nikon ECLIPSE Ti2 | 2026-10-10 12:41:24 | 28 | ||||||||
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RobotReviewer Resource Report Resource Website 1+ mentions |
RobotReviewer (RRID:SCR_021064) | software application, software resource, text-mining software, web application | Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials. | Data automatic extraction, clinical trial reports, automatically extract key data, Evidence Based Medicine, text journal articles processing, randomized controlled trials |
is related to: Northeastern University; Massachusetts; USA is related to: University of Texas at Austin; Texas; USA |
Medical Research Council UK ; NCI UH2 CA203711; NLM R01 LM012086 |
PMID:29093610 DOI:10.1093/jamia/ocv044 |
Free, Available for download, Freely available | https://github.com/ijmarshall/robotreviewer, https://robotreviewer.vortext.systems/ | SCR_021064 | SciCrunch Registry | Automating Biomedical Evidence Synthesis | 2026-10-10 12:41:45 | 1 | ||||||
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cellxgene Resource Report Resource Website 50+ mentions |
cellxgene (RRID:SCR_021059) | data processing software, data visualization software, software application, software resource | Software tool as interactive explorer for single cell transcriptomics datasets. Used to explore and visualize high dimensional single cell datasets in interactive way. Can visualize gene expression at level of entire dataset or particular subset of cells to help identify cell types, which can in turn help identify diseases. Enables plotting gene expression level against another gene to compare how these different genes are expressed across dataset. Open source cell visualization tool integrates with tools like SciPy and Jupyter. | Single cell transcriptomics datasets explorer, gene expression visualization, identify cell types, identify diseases, plotting gene expression level |
is used by: BICCN is related to: Allen Institute for Brain Science |
Free, Available for download, Freely available | https://github.com/chanzuckerberg/cellxgene | SCR_021059 | SciCrunch Registry | 2026-10-10 12:41:45 | 82 | |||||||||
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BioSpherix: Oxycycler GT4181C Controller Resource Report Resource Website 1+ mentions |
BioSpherix: Oxycycler GT4181C Controller (RRID:SCR_021111) | GT4181C | instrument resource | Carbon Monoxide, O2, and CO2 controller that also features limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber Incubator Subchamber from BioSpherix. This system also features secondary monitor for Carbon Monoxide and may be used in combination with I-Hood Incubator Hood from BioSpherix for ventilating fumes. | Carbon Monoxide, O2, CO2, controller, relative humidity limit control, temperature monitoring, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021111.pdf | SCR_021111 | SciCrunch Registry | CO2, Oxycycler GT4181C Dynamic O2, OxyCycler GT4181C, and Carbon Monoxide Subchamber Controller System | 2026-10-10 12:41:17 | 1 | ||||||||
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seqpac Resource Report Resource Website 1+ mentions |
seqpac (RRID:SCR_021079) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for analysis of short sequenced reads. Framework for small RNA analysis in R using Sequence Based Counts.Can be applied on any type of data generated by large scale nucleotide sequencing, where user wish to maintain sequence integrity during whole analysis. | sRNA-seq data analysis, RNA-seq, small RNA, short sequence reads analysis, sequence based counts, nucleotide sequencing data | is related to: R Project for Statistical Computing | Formas - Swedish Research Council for Sustainable Development 2020-01042; Knut and Alice Wallenberg Stiftelse ; 2015.0165; Ragnar Söderberg ; The Swedish Research Council 2015-03141 |
DOI:10.1101/2021.03.19.436151 | Free, Available for download, Freely available | SCR_021079 | SciCrunch Registry | 2026-10-10 12:41:16 | 1 | ||||||||
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BioSpherix: OxyCycler GT41 Controller Resource Report Resource Website |
BioSpherix: OxyCycler GT41 Controller (RRID:SCR_021110) | GT41 | instrument resource | O2 and CO2 controller that also features relative humidity limit control and monitoring of temperature conditions when used in combination with C-Chamber Incubator subchamber from BioSpherix. | Relative humidity limit control, temperature conditions monitoring, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021110.pdf | SCR_021110 | SciCrunch Registry | CO2, OxyCycler GT41, and RH Subchamber Controller System, OxyCycler GT41 Dynamic O2 | 2026-10-10 12:41:25 | 0 | ||||||||
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BioSpherix: OxyCycler C42 Controller Resource Report Resource Website |
BioSpherix: OxyCycler C42 Controller (RRID:SCR_021109) | C-42 | instrument resource | Incubator controls dynamic or static levels of O2 and CO2 and offers O2 and CO2 profiling. Dual channel and dual gas controller for incubators and C-Chambers. Oxygen and carbon dioxide control is managed via independently programmable channels for optimum control. Applications of OxyCycler C42 incubator controller include intermittent hypoxia, graded hypoxia, and timed hyperoxia.Comes with computer software for easy interface, real time trend charting, data logging, and remote operation. | BioSpherix Ltd, incubator controller, O2 profiling, CO2 profiling, C-Chamber controller, intermittent hypoxia, graded hypoxia, timed hyperoxia, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021109.pdf | SCR_021109 | SciCrunch Registry | OxyCycler C42 Dynamic O2 and CO2 Subchamber Controller, OxyCycler C42 | 2026-10-10 12:41:46 | 0 | ||||||||
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Hifiasm Resource Report Resource Website 500+ mentions |
Hifiasm (RRID:SCR_021069) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as haplotype resolved de novo assembler for PacBio Hifi reads. Can assemble human genome in several hours.Introduces new graph binning algorithm and achieves haplotype resolved assembly given trio data. Takes advantage of long high fidelity sequence reads to represent haplotype information in phased assembly graph. Preserves contiguity of all haplotypes. | PacBio Hifi reads, haplotype resolved de novo assembler, trio data, long high fidelity sequence reads, | NHGRI R01 HG010040; NHGRI U01 HG010961; NHGRI U41HG010972 |
PMID:33526886 | Free, Available for download, Freely available | SCR_021069 | SciCrunch Registry | 2026-10-10 12:41:16 | 584 | |||||||||
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GenAlEx Resource Report Resource Website 50+ mentions Issue |
GenAlEx (RRID:SCR_021102) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level. | population genetic analyses, Microsoft Excel, diploid codominant analysis, haploid genetic loci, binary genetic loci, DNA sequences analysis | PMID:22820204 | Free, Available for download, Freely available | SCR_021102 | SciCrunch Registry | GenAlEx 6.5, Genetic Analysis in Excel | 2026-10-10 12:41:25 | 79 |
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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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