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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-09-05 06:31:28 | 740 | |||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | data processing software, software application, software resource | Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows. | trimming, task, paired, end, single, data, next, generation, sequencing, filtering, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill |
BLE/BMELV Verbundprojekt ; BMBF |
PMID:24695404 DOI:10.1093/bioinformatics/btu170 |
biotools:trimmomatic, OMICS_01097 | https://omictools.com/trimmomatic-tool, https://bio.tools/trimmomatic, https://sources.debian.org/src/trimmomatic/ | SCR_011848 | Trimmomatic v 0.32 | 2026-09-05 06:30:47 | 23444 | |||||
|
ImageQuant Resource Report Resource Website 5000+ mentions |
ImageQuant (RRID:SCR_014246) | IQTL | data processing software, image analysis software, software application, software resource | Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automatic image analysis, general image analysis, image analysis software |
is listed by: SoftCite has parent organization: GE Healthcare |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014246 | ImageQuant TL | 2026-09-05 06:30:48 | 9231 | ||||||||
|
ImageScope Resource Report Resource Website 1000+ mentions |
ImageScope (RRID:SCR_014311) | data processing software, image analysis software, software application, software resource | Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | slide image modification, viewing program |
is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | http://www.leicabiosystems.com/digital-pathology/digital-pathology-management/imagescope/ | SCR_014311 | 2026-09-05 06:30:48 | 3691 | |||||||||
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ATSAS Resource Report Resource Website 1000+ mentions |
ATSAS (RRID:SCR_015648) | data processing software, software application, software resource, software toolkit | Software toolkit for small-angle scattering data analysis from biological macromolecules. | macromolecule, small-angle scattering, ab initio method, rigid body modeling, pbd oriented tool, mixture, flexible system |
is listed by: SoftCite is related to: DAMMIF |
PMID:28808438 | SCR_015648 | Data Analysis Software ATSAS | 2026-09-05 06:30:50 | 1377 | |||||||||
|
ProteinLynx Global Server Resource Report Resource Website 100+ mentions |
ProteinLynx Global Server (RRID:SCR_016664) | PLGS | data or information resource, organization portal, portal, service resource | Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems. | Waters Corporation, quantitative, qualitative, proteomics, research, system | is listed by: SoftCite | SCR_016664 | ProteinLynx Global SERVER™ (PLGS), ProteinLynx Global Server, PLGS, ProteinLynx Global Server (PLGS), Protein Lynx Global Server 2.4, Protein Lynx Global Server | 2026-09-05 06:30:51 | 215 | |||||||||
|
Maestro Resource Report Resource Website 50+ mentions |
Maestro (RRID:SCR_016748) | data or information resource, portal | Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data. | molecular, modeling, environment, computation, data, analyze, organize |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Trial available | SCR_016748 | 2026-09-05 06:30:52 | 88 | ||||||||||
|
BlobFinder Resource Report Resource Website 100+ mentions |
BlobFinder (RRID:SCR_015788) | data processing software, image analysis software, software application, software resource | Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell. | fluorescence, microscopy, average count analysis, single cell analysis, cell calculation |
is listed by: SoftCite has parent organization: Uppsala University; Uppsala; Sweden |
Free, Available for download, Runs on Windows, Tutorial available | SCR_015788 | 2026-09-05 06:30:50 | 129 | ||||||||||
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Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | data processing software, software application, software resource | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-09-05 06:30:52 | 39 | ||||||
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HALO Resource Report Resource Website 100+ mentions |
HALO (RRID:SCR_018350) | HALO | data processing software, image analysis software, software application, software resource | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-09-05 06:30:55 | 108 | ||||||||
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HaploReg Resource Report Resource Website 1000+ mentions |
HaploReg (RRID:SCR_006796) | HaploReg | data or information resource, database | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. | chromatin state, conservation, regulatory motif, alteration, variant, chromatin, motif, annotation, genome, variation, genome-wide association study, refsnp, refseq gene, snp, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Broad Institute |
NHGRI R01-HG004037; NHGRI RC1-HG005334; NSF 0644282 |
PMID:22064851 | biotools:HaploReg, nlx_151407 | http://compbio.mit.edu/HaploReg, https://bio.tools/HaploReg | SCR_006796 | 2026-09-05 06:31:36 | 1048 | ||||||
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REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | software resource, web application | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-09-05 06:30:20 | 23733 | |||||
|
RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, software resource, web service | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/, http://www.rnalocate.org/ | SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-09-05 06:30:30 | 24 | ||||||
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SRAMP Resource Report Resource Website 100+ mentions |
SRAMP (RRID:SCR_024500) | simulation software, software application, software resource | Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. | mammalian m(6)A site predictor, sequence derived features based predictor, | is listed by: SoftCite | PMID:26896799 | Free, Available for download, Freely available | SCR_024500 | Sequence-based Rna Adenosine Methylation site Predictor | 2026-09-05 06:30:31 | 452 | ||||||||
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RNAfold Resource Report Resource Website 100+ mentions |
RNAfold (RRID:SCR_024427) | data access protocol, software resource, web service | Web server predict secondary structures of single stranded RNA or DNA sequences. | predict secondary structures, single stranded RNA, DNA sequences, | is listed by: SoftCite | Free, Freely available | SCR_024427 | 2026-09-05 06:30:31 | 100 | ||||||||||
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Nano Measurer Resource Report Resource Website 1+ mentions |
Nano Measurer (RRID:SCR_024493) | data analysis software, data processing software, software application, software resource | Software tool to process micrograph images for particle size. | process micrograph images, images for particle size, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024493 | 2026-09-05 06:30:31 | 9 | ||||||||||
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ToposPro Resource Report Resource Website 10+ mentions |
ToposPro (RRID:SCR_024496) | data analysis software, data processing software, software application, software resource | Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters. | geometrical and topological properties analysis, crystals, networks, tilings, periodic structures analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024496 | 2026-09-05 06:30:31 | 18 | ||||||||||
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Stem Resource Report Resource Website 1+ mentions |
Stem (RRID:SCR_024499) | data analysis software, data processing software, software application, software resource | Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology. | short time series gene expression data analysis, clustering, comparing, visualizing, short time series gene expression data, microarray experiments data, identify temporal expression profiles identify genes associated with expression profiles, compare behavior of genes across multiple conditions, | is listed by: SoftCite | PMID:16597342 | Free, Available for download, Freely available | SCR_024499 | Short Time-series Expression Miner | 2026-09-05 06:30:31 | 6 | ||||||||
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Agilent Seahorse Wave Resource Report Resource Website 10+ mentions |
Agilent Seahorse Wave (RRID:SCR_024491) | data acquisition software, data processing software, software application, software resource | Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis. | Instrument control, data acquisition, Agilent Seahorse XFe96 analyzer, Agilent Seahorse XFe24 analyzer, predefined assay templates, streamlined experimental design, simplified metabolic analysis, | is listed by: SoftCite | SCR_024491 | Seahorse Wave | 2026-09-05 06:30:31 | 27 | ||||||||||
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lDDT Resource Report Resource Website 1+ mentions |
lDDT (RRID:SCR_024524) | data access protocol, software resource, web service | Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility. | local superposition free score, comparing protein structures and models, distance difference tests, | is listed by: SoftCite | PMID:23986568 | Free, Freely available | SCR_024524 | Local Distance Difference Test | 2026-09-05 06:30:32 | 2 |
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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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