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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NanoString: GeoMx Digital Spatial Profiler Resource Report Resource Website 10+ mentions |
NanoString: GeoMx Digital Spatial Profiler (RRID:SCR_021660) | GeoMx DSP | instrument resource | Integrated commercial system comprising hardware, software and nCounter chemistry that enables simultaneous, highly multiplex spatial profiling of proteins or RNA in FFPE tissues. DSP platform quantifies abundance of protein or RNA by counting unique indexing oligonucleotides assigned to each target of interest. Used to rapidly and quantitatively assess biological implications of heterogeneity within tissue samples. | Spatial profiling, proteins spatial profiling, RNA spatial profiling, NanoString, counting unique indexing oligonucleotides, tissue heterogeneity, Digital Spatial Profiler, instrument, equipment, USEDit | is listed by: USEDit | PMID:32393914 | Restricted | SCR_021660 | GeoMx Digital Spatial Profiler | 2026-08-01 12:07:22 | 21 | |||||||
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Hamamatsu: NanoZoomer 2.0-HT Resource Report Resource Website 10+ mentions |
Hamamatsu: NanoZoomer 2.0-HT (RRID:SCR_021658) | instrument resource | High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically. | Hamamatsu, digital scanner, full slide scanner, 210 slides process, automatic scanner, instrument, equipment, USEDit | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021658.pdf | Model_Number_NanoZoomer_2.0-HT | SCR_021658 | Hamamatsu NanoZoomer 2.0-HT System | 2026-08-01 12:07:22 | 25 | ||||||||
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ontquery Resource Report Resource Website 1+ mentions |
ontquery (RRID:SCR_021659) | software resource | Software tool as framework querying ontology terms within SciCrunch and SciCrunch SciGraph endpoints. | Querying ontology terms, ontology terms, SciCrunch SciGraph endpoints, querying ontology | Free | https://github.com/tgbugs/ontquery | SCR_021659 | 2026-08-01 12:07:14 | 1 | ||||||||||
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McKinley: Cellometer Auto T4 Resource Report Resource Website 1+ mentions |
McKinley: Cellometer Auto T4 (RRID:SCR_021656) | instrument resource | System includes automated cell counter for trypan blue viability for cell lines and bright field imaging and pattern recognition software to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported. | Automated cell counter, trypan blue cell viability, bright field imaging, pattern recognition, count individual cells, cell concentration count, cell diameter count, instrument, equipment, USEDit | is listed by: USEDit | Commercially available | Model_Number_Auto_T4 | SCR_021656 | Auto T4, Nexcellom Bioscience Cellometer Auto T4 Bright Field Cell Counter, Cellometer Auto T4 Bright Field Cell Counter | 2026-08-01 12:07:14 | 2 | ||||||||
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GE: Amersham Imager 600 Resource Report Resource Website 1+ mentions |
GE: Amersham Imager 600 (RRID:SCR_021853) | instrument resource | Amersham Imager 600 is CCD camera system that produces digitial images of samples in gels or membranes in three different modes: chemiluminescence, colorimetric and fluorescent image capture. Provides imaging system to capture and analyze protein and DNA sample gels and membranes in high resolution. | USEDit, chemiluminescence, colorimetric, fluorescent, image capture, digitial images | is listed by: USEDit | Commercially available | https://photos.labwrench.com/equipmentManuals/19468-6742.pdf | SCR_021853 | GE Healthcare Amersham Imager 600, Amersham Imager 600 | 2026-08-01 12:07:25 | 7 | ||||||||
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BorutaShap Resource Report Resource Website 1+ mentions |
BorutaShap (RRID:SCR_021696) | software resource | Software tool as wrapper feature selection method which combines both Boruta feature selection algorithm with shapley values. | Wrapper feature selection method, Boruta feature selection algorithm, shapley values | Free, Available for download, Freely available | https://github.com/Ekeany/Boruta-Shap | SCR_021696 | 2026-08-01 12:07:23 | 6 | ||||||||||
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LightGBM Resource Report Resource Website 10+ mentions |
LightGBM (RRID:SCR_021697) | software resource | Software tool as gradient boosting framework that uses tree based learning algorithms. Designed to be distributed and efficient with advantages:Faster training speed and higher efficiency;Lower memory usage;Better accuracy;Support of parallel, distributed, and GPU learning;Capable of handling large scale data. | Gradient boosting framework | Free, Available for download, Freely available | https://github.com/Microsoft/LightGBM/blob/master/docs/index.rst | SCR_021697 | 2026-08-01 12:07:16 | 14 | ||||||||||
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pyxDamerauLevenshtein Resource Report Resource Website 1+ mentions |
pyxDamerauLevenshtein (RRID:SCR_021858) | software resource | Software tool implements Damerau-Levenshtein (DL) edit distance algorithm for Python in Cython for high performance. | Damerau-Levenshtein, edit distance algorithm | Free, Available for download, Freely available | SCR_021858 | 2026-08-01 12:07:18 | 1 | |||||||||||
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Phenex Resource Report Resource Website |
Phenex (RRID:SCR_021748) | software resource | Software application for annotating character matrix files with ontology terms. Character states can be annotated using Entity-Quality syntax, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from taxonomy ontology. Phenex saves ontology annotations alongside original free text character matrix data using new NeXML format standard for evolutionary data. | phenotype, ontology, taxonomy ontology, taxa, ontology annotations, free text character matrix data, NeXML, evolutionary data | NSF DBI 0641025; NHGRI HG002659; NSF EF0423641 |
DOI:10.1371/journal.pone.0010500 | Free, Available for download, Freely available | https://github.com/phenoscape/Phenex/wiki#download--installation | SCR_021748 | 2026-08-01 12:07:17 | 0 | ||||||||
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NanoString: nCounter Analysis System Resource Report Resource Website 10+ mentions |
NanoString: nCounter Analysis System (RRID:SCR_021712) | nCounter | instrument resource | System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification. | Multiplex analysis, RNA analysis, DNA analysis, Protein analysis, NanoString Differential Expression, NanoString, analysis system, instrument, equipment, USEDit, ABRF | is listed by: USEDit | Commercially available | SCR_021712 | nCounter Analysis System, Bruker nCounter Analysis System | 2026-08-01 12:07:16 | 29 | ||||||||
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YAML Resource Report Resource Website 10+ mentions |
YAML (RRID:SCR_021710) | software resource | YAML is a human friendly data serialization language for all programming languages. Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing. | Data serialization language, common native data types, agile programming languages, configuration files, Internet messaging, object persistence, data auditing | Free, Freely available | https://yaml.org/spec/1.2.1/ | SCR_021710 | YAML 1.2 | 2026-08-01 12:07:23 | 17 | |||||||||
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TriKinetics: Drosophila Activity Monitoring System Resource Report Resource Website 1+ mentions |
TriKinetics: Drosophila Activity Monitoring System (RRID:SCR_021798) | instrument resource | System from TriKinetics for monitoring Drosophila activity. Includes hardware and DAMSystem3 Software for data acquision and DAMFileScan Software for scanning data for errors. Applied to behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity. | monitoring Drosophila activity, behavioral activity experiment, behavioral activity, activity monitoring |
is related to: TriKinetics DAMSystem3 Software is related to: Trikinetics DAM FileScan |
DOI:10.1101/pdb.prot5518 | Restricted | SCR_021798 | Drosophila Activity Monitoring System, DAM, DAM System, Drosophila Activity Monitor | 2026-08-01 12:07:24 | 9 | ||||||||
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Trikinetics DAM FileScan Resource Report Resource Website 1+ mentions |
Trikinetics DAM FileScan (RRID:SCR_021817) | software resource | Software tool used in Drosophila Activity Monitor system to scann data for errors. Also allows user to extract data from monitor files and bin data in different lengths. | scann data for errors, Drosophila Activity Monitor system, extract data | is related to: TriKinetics: Drosophila Activity Monitoring System | SCR_021817 | DAM FileScan | 2026-08-01 12:07:18 | 1 | ||||||||||
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Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands Resource Report Resource Website 1+ mentions |
Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands (RRID:SCR_021706) | institution | Institute is entirely devoted to psycholinguistics – the study of how we produce and understand language, and how we acquire these skills as first or second language learners. The only institution in the world entirely dedicated to psycholinguistics, and is also one of only three among total of 90 within the Max Planck Society to be located outside Germany. |
has parent organization: Max-Planck-Gesellschaft is parent organization of: ELAN |
SCR_021706 | 2026-08-01 12:07:23 | 1 | ||||||||||||
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ELAN Resource Report Resource Website 10+ mentions |
ELAN (RRID:SCR_021705) | software resource | Software annotation tool for audio and video recordings. Annotation can be sentence, word or gloss, comment, translation or description of any feature observed in media. Annotations can be created on multiple layers. Tiers can be hierarchically interconnected. Annotation can either be time-aligned to media or it can refer to other existing annotations. Content of annotations consists of Unicode text and annotation documents are stored in XML format (EAF). | Annotation tool, audio recordings, video recordings, Unicode text, annotation documents, documents stored, XML format | has parent organization: Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands | Free, Available for download, Freely available | SCR_021705 | 2026-08-01 12:07:15 | 19 | ||||||||||
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Seq-N-Slide Resource Report Resource Website 10+ mentions |
Seq-N-Slide (RRID:SCR_021752) | software resource | Set of automated workflows for common sequencing based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening. Sequencing data analysis pipelines. | Sequencing data analysis pipelines | Free, Available for download, Freely available | SCR_021752 | 2026-08-01 12:07:24 | 16 | |||||||||||
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Halvade Somatic Resource Report Resource Website 1+ mentions |
Halvade Somatic (RRID:SCR_021771) | software resource | Software implements germline and somatic variant calling pipelines based on best practices pipelines from Broad Institute using Spark framework. Produces VCF output file which contains single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by used tools. Program requires Spark on either local cluster with one or more nodes, Amazon EMR cluster or Docker image to run. | somatic variant, GATK, Halvade, VCF output file, germline, somatic variant calling, Spark framework | uses: GATK | Free, Available for download, Freely available | SCR_021771 | Halvade for Spark | 2026-08-01 12:07:24 | 1 | |||||||||
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Online Kappa Calculator Resource Report Resource Website 1+ mentions |
Online Kappa Calculator (RRID:SCR_021770) | software resource | Software tool can be used to calculate kappa, chance adjusted measure of agreement, for any number of cases, categories, or raters. | Calculator, calculate kappa, chance adjusted measure of agreement, number of cases, number of categories, number of | Free, Freely available | SCR_021770 | 2026-08-01 12:07:16 | 8 | |||||||||||
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CellScale: MicroTester G2 system Resource Report Resource Website 1+ mentions |
CellScale: MicroTester G2 system (RRID:SCR_022034) | instrument resource | System includes MicroTester G2 device and software. MicroTester G2 is mechanical test device that can be used to test properties of variety of tissues and materials. Main components of device are load application microbeam, actuators, imaging system, and fluid bath/test chamber. MicroTester G2 software is divided into two modules: data collection module and review and analysis module. | instrument, equipment, USEDit, CellScale, mechanical test device, test properties, tissues, materials | is listed by: USEDit | Restricted | https://www.cellscale.com/downloads2/MicroTester%20User%20ManualG2.pdf | SCR_022034 | SquisherJoy | 2026-08-01 12:07:28 | 3 | ||||||||
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Shahid Sadoughi University of Medical Sciences; Yazd; Iran Resource Report Resource Website 1+ mentions |
Shahid Sadoughi University of Medical Sciences; Yazd; Iran (RRID:SCR_022031) | university | Public university located in center of Iran in World Heritage city of Yazd. | SCR_022031 | Shahid Sadoughi University of Medical Sciences | 2026-08-01 12:07:21 | 1 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
