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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FuzzyWuzzy Resource Report Resource Website 1+ mentions |
FuzzyWuzzy (RRID:SCR_021699) | data analytics software, software application, software resource, software toolkit | Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching. | Levenshtein Distance, calculate differences between sequences, string matching | Free, Freely available | SCR_021699 | SciCrunch Registry | 2026-10-31 12:18:18 | 5 | |||||||||||
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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 | SciCrunch Registry | GE Healthcare Amersham Imager 600, Amersham Imager 600 | 2026-10-31 12:18:17 | 9 | ||||||||
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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 | SciCrunch Registry | 2026-10-31 12:18:23 | 7 | ||||||||||
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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 | SciCrunch Registry | 2026-10-31 12:18:14 | 28 | ||||||||||
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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 | SciCrunch Registry | 2026-10-31 12:18:16 | 1 | |||||||||||
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PaintOmics Resource Report Resource Website 10+ mentions |
PaintOmics (RRID:SCR_021859) | data access protocol, software resource, web service | Web tool for integrative visualization of multiple omic datasets onto KEGG pathways. Supports integrated visualization of multiple species of different biological kingdoms and offers user possibility to request any other organism present in KEGG database. | integrative visualization, multiple omic datasets, KEGG pathways, multiple species | GVA-FEDER ; Spanish Ministry of Science and Innovation |
DOI:10.1093/bioinformatics/btq594 PMID:29800320 |
Free, Freely available | SCR_021859 | SciCrunch Registry | PaintOmics 3, Paintomics | 2026-10-31 12:18:21 | 15 | ||||||||
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PI Motion Control Software Resource Report Resource Website |
PI Motion Control Software (RRID:SCR_021867) | software resource | Software to control positioning systems without their own macro facility. | Physik Instrumente, control positioning systems, without their own macro facility | Restricted | SCR_021867 | SciCrunch Registry | Physik Instrumente Motion Control Software, Motion Control Software | 2026-10-31 12:18:17 | 0 | ||||||||||
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Sample Size Shop Resource Report Resource Website 1+ mentions |
Sample Size Shop (RRID:SCR_021747) | data or information resource, portal, topical portal | Platform for multilevel and longitudinal data.Provide researchers such as behavioral and social scientists with tools and education related to study design including Calculating power and sample size for any univariate or multivariate test for general linear multivariate model, assuming fixed predictors;Producing confidence intervals on power estimates for designs with fixed predictors;Producing power calculations for designs with single Gaussian covariate;Supporting designs with unequal group sizes, and complicated covariance structures;Creating basic power curves. | multilevel data, longitudinal data, calculating power and sample size, producing confidence intervals on power estimates, producing power calculations, creating basic power curves | Free, Freely available | SCR_021747 | SciCrunch Registry | 2026-10-31 12:18:15 | 4 | |||||||||||
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ANGSD Resource Report Resource Website 10+ mentions |
ANGSD (RRID:SCR_021865) | data analysis software, data processing software, software application, software resource | Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods. | analysing NGS data, next generation sequencing data analysis, raw sequencing data, genotype likelihoods | DOI:10.1186/s12859-014-0356-4 | Free, Available for download, Freely available | http://www.popgen.dk/angsd/index.php/ANGSD | SCR_021865 | SciCrunch Registry | Analysis of Next Generation Sequencing Data | 2026-10-31 12:18:21 | 47 | ||||||||
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Arthropoda Assembly Assessment Catalog Resource Report Resource Website 1+ mentions |
Arthropoda Assembly Assessment Catalog (RRID:SCR_021864) | a3cat, A3Cat | catalog, data or information resource, database | Database of metadata and assembly quality metrics for all Arthropod assemblies on NCBI. | Metadata and assembly quality metrics, Arthropod assemblies, NCBI | DOI:10.1101/2021.10.15.464561 | Free, Available for download, Freely available | https://gitlab.com/evogenlab/a3cat-workflow | SCR_021864 | SciCrunch Registry | Arthropoda Assembly Assessment Catalogue | 2026-10-31 12:18:16 | 2 | |||||||
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Platform for Epigenomic and Genomic Research Resource Report Resource Website 1+ mentions |
Platform for Epigenomic and Genomic Research (RRID:SCR_021861) | PEGR | data access protocol, software resource, web service | Web service platform logging metadata for genomic samples and high throughput sequencing, manages data processing workflows, and provides quality control reporting and visualization. PEGR links people, samples, protocols, sequencing and bioinformatics computation to comply with FAIR best practices for publications and data management plans.Tracks and quality controls experiments from conception to publication ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at wet bench, while continuing to fully support reproducibility and reliability for bioinformaticians through integration with Galaxy platform. | FAIR compliance, platform logging metadata, genomic samples, high throughput sequencing, experiments quality controls, tracking experiments, rigor and reproducibility support | DOI:10.1101/2021.07.26.453821 | Free, Available for download, Freely available | SCR_021861 | SciCrunch Registry | 2026-10-31 12:18:25 | 8 | |||||||||
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Phenex Resource Report Resource Website 1+ mentions |
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 | NHGRI HG002659; NSF DBI 0641025; NSF EF0423641 |
DOI:10.1371/journal.pone.0010500 | Free, Available for download, Freely available | https://github.com/phenoscape/Phenex/wiki#download--installation | SCR_021748 | SciCrunch Registry | 2026-10-31 12:18:19 | 1 | ||||||||
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Trialdesign Resource Report Resource Website 10+ mentions |
Trialdesign (RRID:SCR_021749) | data or information resource, portal, topical portal | Integrated platform for designing clinical trials. | Clinical trial, education, training, study design, innovative adaptive clinical trial designs | Free, Freely available | SCR_021749 | SciCrunch Registry | Trialdesign.org | 2026-10-31 12:18:15 | 17 | ||||||||||
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FlashPCA Resource Report Resource Website 10+ mentions Issue |
FlashPCA (RRID:SCR_021680) | data analysis software, data processing software, software application, software resource | Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets. | Principal component analysis, large scale genome wide data, single nucleotide polymorphism data, biobank scale genotype datasets | DOI:10.1093/bioinformatics/btx299 DOI:10.1371/journal.pone.0093766 |
Free, Available for download, Freely available | SCR_021680 | SciCrunch Registry | FlashPCA2 | 2026-10-31 12:18:14 | 38 | |||||||||
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Aquaria Resource Report Resource Website |
Aquaria (RRID:SCR_021834) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application to help biologists use 3D structures to gain insight into protein function. Used in revealing novel insights into molecular mechanisms underlying protein function in health and disease. System for incorporating 3D structures into variant analysis. | molecular mechanisms underlying protein function, incorporating 3D structures into variant analysis | is related to: Aquaria COVID Resource | DOI:10.1101/2021.09.10.459756 | Free, Freely available | https://aquaria.app | SCR_021834 | SciCrunch Registry | Aquaria.App | 2026-10-31 12:18:16 | 0 | |||||||
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Aquaria COVID Resource Resource Report Resource Website |
Aquaria COVID Resource (RRID:SCR_021835) | data access protocol, software resource, web service | Web tool to visually summarise all available 3D structural information for all proteins comprising COVID-19 virus (SARS-CoV-2). Resource also gives access to structural models, generated by finding all sequence regions with detectable similarity to any currently published 3D structure. These structures are clustered into distinct states that provide insight into viral replication, mimicry, and hijacking. | 3D protein structural information, COVID-19, SARS-CoV-2, structural models | is related to: Aquaria | Free, Freely available | https://aquaria.ws/covid, https://aquaria.ws/covid#info | SCR_021835 | SciCrunch Registry | Aquaria-COVID Resource | 2026-10-31 12:18:21 | 0 | ||||||||
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Microns Explorer Resource Report Resource Website 10+ mentions |
Microns Explorer (RRID:SCR_021678) | data or information resource, portal, topical portal | Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons. | Connectome, mouse, cortex, electron microscopy, functional imaging data, cortical circuitry reconstruction, neuron |
is related to: Allen Institute for Brain Science is related to: Princeton University; New Jersey; USA is related to: Baylor College of Medicine; Houston; Texas |
IARPA MICrONS | Free, Freely available | SCR_021678 | SciCrunch Registry | MICrONS Explorer | 2026-10-31 12:18:14 | 19 | ||||||||
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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 | SciCrunch Registry | nCounter Analysis System, Bruker nCounter Analysis System | 2026-10-31 12:18:15 | 36 | ||||||||
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StimGen Resource Report Resource Website 1+ mentions |
StimGen (RRID:SCR_021676) | data processing software, data visualization software, software application, software resource | Software tool as interface for designing and presenting visual stimuli. | Retina, Visual Stimulation, Design, Presentation | SCR_021676 | SciCrunch Registry | 2026-10-31 12:18:23 | 3 | ||||||||||||
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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 | SciCrunch Registry | YAML 1.2 | 2026-10-31 12:18:19 | 23 |
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