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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Olympus FV10-ASW Viewer Resource Report Resource Website 10+ mentions |
Olympus FV10-ASW Viewer (RRID:SCR_024433) | data processing software, image processing software, software application, software resource | Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read. | FV1200/FV1000/FV500/FV300 microscopes image processing, FV1200/FV1000/FV500/FV300 microscopes data processing, FV file format, | Free, Available for download, Freely available | https://www.olympus-lifescience.com/ | SCR_024433 | FV10-ASW Viewer software v4.2b | 2026-08-29 11:28:28 | 39 | |||||||||
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XDD Resource Report Resource Website |
XDD (RRID:SCR_024434) | software resource | Software digital library and cyberinfrastructure facilitating discovery and utilization of data and knowledge in published documents. | digital library and cyberinfrastructure, discovery and utilization of data and knowledge, data and knowledge in published documents, | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | Free, Frely available | SCR_024434 | 2026-08-29 11:28:28 | 0 | ||||||||||
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Molecular Property Diagnostic Suite Covid-19 Resource Report Resource Website 1+ mentions |
Molecular Property Diagnostic Suite Covid-19 (RRID:SCR_024545) | MPDS-Covid19 | data or information resource, disease-related portal, portal, topical portal | Galaxy based disease specific web portal for drug discovery research of COVID-19. Open access disease specific drug discovery portal. | Drug discovery, disease specific drug discovery, COVID-19 | Covid-19 | Department of Biotechnology Govt. of India | DOI:10.1101/2023.08.29.555437 | Free, Freely available | SCR_024545 | Galaxy MPDS COVID-19 | 2026-08-29 11:28:14 | 1 | ||||||
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ScanProsite Resource Report Resource Website 100+ mentions |
ScanProsite (RRID:SCR_024425) | PMID:16845026 | data access protocol, software resource, web service | Web tool for detecting PROSITE signature matches in protein sequences. | detecting PROSITE signature matches, protein sequences, | is listed by: SoftCite | Swiss National Science Foundation ; Swiss Federal Government |
Free, Freely available | https://www.expasy.org/resources/scanprosite | SCR_024425 | 2026-08-29 11:28:28 | 106 | |||||||
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BatchEval Resource Report Resource Website 1+ mentions |
BatchEval (RRID:SCR_024546) | data analysis software, data processing software, software application, software resource | Software tool for evaluating batch effects in data integration. Tool to improve accuracy and reliability of experimental results. Used to evaluate batch effect of dataset integration and output comprehensive report. | evaluating batch effects in data integration, evaluating batch effects, data integration, improve accuracy and reliability, experimental results, | Free, Available for download, Freely available | SCR_024546 | 2026-08-29 11:28:14 | 1 | |||||||||||
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Kassandra Resource Report Resource Website 1+ mentions |
Kassandra (RRID:SCR_024548) | data analysis software, data processing software, software application, software resource | Software bulk RNA-seq cellular deconvolution tool. Used for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing gene expression. | RNA-seq cellular deconvolution, analysis of healthy tissue and tumor biopsies, RNA-seq NGS data, predict cellular composition, analyzing gene expression, | BostonGene | PMID:35944503 | Free, Available for download, Freely available | https://github.com/BostonGene/Kassandra | SCR_024548 | 2026-08-29 11:28:29 | 5 | ||||||||
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LFP Monitoring Resource Report Resource Website |
LFP Monitoring (RRID:SCR_024428) | instrument resource, software resource, source code | Low cost platform for multianimal chronic Local Field Potential video monitoring with Graphical User Interface for seizure detection and behavioral scoring. Enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real time, and parses recorded data into manageable file sizes. Hardware solution leverages Intan and Open Ephys acquisition systems and software solution is implemented in Bonsai. Data are synchronized and parsed in Bonsai, allowing for flexibility and scalability of up to 128 channels per animal. The use of Intan adapter board for LFP video recordings allows compatibility with large variety of recording devices. Custom made electrodes and cables were components for the chronic LFP recordings. Used as acquisition system for long term video neurophysiology recordings. | OpenBehavior, acquisition system, long term video neurophysiology recordings, seizure detection, behavioral scoring, multianimal chronic Local Field Potential, video monitoring, LFP video recording, Graphical User Interface for seizure detection and behavioral scoring, Intan adapter board, Open Ephys acquisition system, Bonsai, custom made electrodes and cables, instrument, device, | is listed by: OpenBehavior | PMID:36192155 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/lfpmonitoring/ | SCR_024428 | Local Field Potential video Monitoring | 2026-08-29 11:28:10 | 0 | |||||||
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Tecan: Infinite M200 Resource Report Resource Website 1+ mentions |
Tecan: Infinite M200 (RRID:SCR_024560) | instrument resource | TECAN Infinite M200 is laboratory device and accessory for multiplex luminescence and fluorescence applications. Device features automated robotic arm for dispensing samples or reagents onto cuvettes or microplates, as well as range of high speed and throughput sample injection capabilities. Infinite M200 is integrated with TECAN's proven laser-based multi-channel detection technology, to measure multiple biological responses simultaneously. System features graphical user interface to configure instrument for single or multiple sample injection processes. Accommodates range of different cuvette and microplate vessels, suitable for both 1.5ml and 0.2ml tubes as well as plates up to 384 wells. Multichannel optical detector can detect up to four different signals in parallel, with wide range of detection wavelengths. Designed for high-throughput applications with sensitive fluorescence and luminescence. Features automated sample injection unit that enables hands-free operation of 96 or 1,536 up to eight-channel multipoint experiments, providing maximum flexibility. Comes with range of software, including intuitive data collection and analysis interface. Designed with automated calibration settings, providing reliable, accurate and reproducible results. | Tecan, laboratory device, multiplex luminescence and fluorescence applications, automated dispenser, sample injection, cuvettes, microplates, tubes, automated sample injection, signals detection, | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_024560.pdf | Model_Number_Infinite_M200 | SCR_024560 | TECAN Infinite M200, Infinite M200 | 2026-08-29 11:28:15 | 4 | ||||||||
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Tecan: NanoQuantPlate Resource Report Resource Website 1+ mentions |
Tecan: NanoQuantPlate (RRID:SCR_024561) | instrument resource | Device designed for simultaneous measurement of multiple low volume samples. Consists of 16 precision manufactured quartz optics in user friendly format, offering precise, straightforward absorbance and fluorescence based measurements from sample volumes as low as 2 µl. Combined with Tecan’s Infinite series readers – the Infinite 200 PRO, Infinite F500 and Infinite M1000 PRO – the NanoQuant Plate provides solution for DNA or RNA quantification, allowing detection of concentrations down to 1 ng/µl for wide variety of applications. | Device, simultaneous measurement of multiple low volume samples, low volume samples, absorbance and fluorescence based measurements, DNA or RNA quantification, low concentration measurement, | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_024561.pdf | Model_Number_NanoQuantPlate | SCR_024561 | 2026-08-29 11:28:29 | 4 | |||||||||
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Leica: TCS SP8 DLS LightSheet microscope Resource Report Resource Website 1+ mentions |
Leica: TCS SP8 DLS LightSheet microscope (RRID:SCR_024563) | instrument resource | Digital LightSheet full confocal with gentle single plane illumination microscope for easy light sheet imaging. TwinFlect mirror deflects illuminating light sheet at 90° angle, which allows integration of illumination and detection beam path into vertical axis of every inverted, Leica TCS SP8 confocal. | Leica, Digital LightSheet, full confocal microscope, light sheet imaging, | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_024563.pdf | SCR_024563 | Leica DLS TCS SP8 | 2026-08-29 11:28:15 | 9 | |||||||||
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DrugSim2DR Resource Report Resource Website 1+ mentions |
DrugSim2DR (RRID:SCR_024564) | simulation software, software application, software resource | Software R package to predict drug functional similarity to drug repurposing. | predict drug functional similarity, similarity to drug repurposing, | is listed by: CRAN | Free, Available for download, Freely available | SCR_024564 | 2026-08-29 11:28:36 | 1 | ||||||||||
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Cancer Information Service Resource Report Resource Website 1+ mentions |
Cancer Information Service (RRID:SCR_024445) | data or information resource, disease-related portal, portal, topical portal | Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information. | Cancer statistics in Japan, National Cancer Center, cancer information, | cancer | Free, Freely available | SCR_024445 | Cancer Information Service in Japan | 2026-08-29 11:28:35 | 1 | |||||||||
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Comprehensive Everglades Restoration Plan Resource Report Resource Website 1+ mentions |
Comprehensive Everglades Restoration Plan (RRID:SCR_024557) | CERP | data or information resource, portal, topical portal | Platform provides framework for restoring, protecting and preserving the greater Everglades ecosystem. The plan is partnership between State of Florida and federal government. | Everglades ecosystem, ecosystem restoring plan, ecosystem protecting plan, ecosystem preserving plan, |
is listed by: DataCite has parent organization: University of California; California; USA |
South Florida Water Management District ; State of Florida |
https://api.datacite.org/dois?prefix=10.25497 | SCR_024557 | South Florida Water Management District Comprehensive Everglades Restoration Plan | 2026-08-29 11:28:29 | 6 | |||||||
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Roche: Cobas C311 Resource Report Resource Website 1+ mentions |
Roche: Cobas C311 (RRID:SCR_024559) | instrument resource | Autoanalyzer is standalone system that provides consolidated testing from range of clinical chemistry applications. Allows determination of sodium, potassium and chloride in serum, plasma and urine using ion selective electrodes. Measurement of HbA1c levels in whole blood can also be performed. | Roche, autoanalyzer, chemistry applications testing, chemicals detection, HbA1c levels detection, sodium, potassium, chloride, serum, plasma, urine, whole blood, ion selective electrodes, | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_024559.pdf | Model_Number_Cobas_C311 | SCR_024559 | 2026-08-29 11:28:36 | 1 | |||||||||
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VSEARCH Resource Report Resource Website 1000+ mentions |
VSEARCH (RRID:SCR_024494) | data analysis software, data processing software, software application, software resource | Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. | processing and preparing metagenomics, genomics and population genomics, nucleotide sequence data, | is listed by: SoftCite | PMID:27781170 | Free, Available for download, Freely available | SCR_024494 | 2026-08-29 11:28:35 | 1553 | |||||||||
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TomoStudio Resource Report Resource Website 1+ mentions |
TomoStudio (RRID:SCR_024498) | data analysis software, data processing software, software application, software resource | Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data. | Tomocube, Inc., Daejeon, . Republic of Korea, visualization and analysis of RI tomograms, color code the image, | is listed by: SoftCite | Restricted | SCR_024498 | 2026-08-29 11:28:28 | 4 | ||||||||||
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SoftCite Resource Report Resource Website |
SoftCite (RRID:SCR_024411) | data or information resource, knowledge base, portal, project portal, software resource | Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale. | Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature, |
lists: ProteinPilot lists: ROCit lists: survivalROC lists: GIFT lists: PyWavelets lists: pRRophetic lists: GOplot lists: Rgdal lists: riskRegression lists: RNAfold lists: RNALocate lists: pyPCcazip lists: ScanProsite lists: RapGreen lists: ABySS lists: AMBER lists: ANNOVAR lists: ASAP lists: ASPicDB lists: AStalavista lists: ATSAS lists: Alien hunter lists: Adobe Photoshop lists: Affymetrix lists: Augustus lists: Argus lists: Adobe Illustrator lists: ART lists: AutoDock Vina lists: AutoDock lists: ANALYZE lists: BLASTClust lists: arrayQualityMetrics lists: BLASTN lists: BLASTX lists: BLASTP lists: Bowtie lists: Autogrid lists: BRB-ArrayTools lists: BEDTools lists: BWA lists: BioEdit lists: BRASS lists: Bioconductor lists: BioExtract lists: BaCelLo lists: BioMoby lists: Brain Extraction Tool lists: Bowtie 2 lists: BoxPlotR lists: biomaRt lists: BioPerl lists: CANGS lists: CFX Manager lists: CEAS lists: BlobFinder lists: CLC Genomics Workbench lists: BREAKDANCER lists: CASAVA lists: CLC Main Workbench lists: ClustalW lists: Clustal W2 lists: ComBat lists: CCP4 lists: Blender lists: Coot lists: CGView lists: COMSOL Multiphysics lists: CTFFIND lists: CalcuSyn lists: ChIPpeakAnno lists: Chimera lists: CVODE lists: DAVID lists: Cufflinks lists: caret lists: ClueGO lists: Cluster lists: Clocklab lists: DIANA-mirPath lists: Cytoscape lists: EMAN lists: E-Prime lists: DESeq2 lists: Definiens Developer XD lists: Eigensoft lists: EMBOSS lists: Ensembl lists: DIALIGN lists: Design-Expert lists: EndNote lists: CMAP lists: EEGLAB lists: CMap lists: Epi Info lists: FASTA lists: Ensembl Genome Browser lists: Epik lists: FACS lists: FCS Express lists: Flowlogic lists: FSL lists: FLASH lists: FATCAT lists: FastQC lists: G*Power lists: GOLD lists: FGENESH lists: FreeSurfer lists: FlowJo lists: GeneTools lists: Galaxy lists: GATK lists: ELDA lists: GraphPad lists: GRADEpro lists: Fiji lists: Gblocks lists: FigTree lists: GENIE lists: GBrowse lists: Gemma lists: GeneChip Operating Software lists: GeneMapper lists: GeneMarker lists: GenABEL lists: GenePattern lists: GraphPad Prism lists: GenePix Pro lists: Google lists: Genesis lists: Hologic lists: GeneSpring GX lists: GeneVenn lists: HaploReg lists: Google Scholar lists: HALO lists: Gwyddion lists: IMAGIC lists: HKL-2000 lists: Glide lists: Glimmer lists: I-TASSER lists: GenomeStudio lists: IMOD lists: Haploview lists: Hmmer lists: Hydra lists: IUPRED lists: HomeCageScan lists: Geneious lists: IGOR Pro lists: IMPUTE lists: Infernal lists: Image-Pro Plus lists: JASP lists: LSM Image Examiner lists: Imaris lists: Image Pro Plus lists: ImageQuant lists: ImageJ lists: Integrative Genomics Viewer lists: jcvi lists: InterProScan lists: KaleidaGraph lists: Ligprep lists: Heidelberg Eye Explorer lists: JMP lists: Ingenuity Pathways Knowledge Base lists: Leica QWin lists: JCB DataViewer lists: Jalview lists: LigandScout lists: Ingenuity Pathway Analysis lists: LabView lists: Kepler lists: MAFFT lists: Jmol lists: ImageScope lists: MACS lists: Maq lists: MUMmer lists: MATLAB lists: Mimics lists: MACH lists: MCODE lists: Mascot lists: Maestro lists: MSQuant lists: MediaWiki lists: MINC lists: MRIcron lists: MOE lists: ModFit LT lists: LIMMA lists: MassLynx lists: mitopred lists: MrBayes lists: MolProbity lists: MUSCLE lists: MutationAssessor lists: MaxQuant lists: Minitab lists: MODELLER lists: MetaboAnalyst lists: MedCalc lists: Origin lists: MPlus lists: MutationTaster lists: MuTect lists: Multi Gauge lists: NIA Array Analysis lists: NIH Image lists: Phenix lists: MycoBank lists: OpenClinica lists: Nexus lists: OMTools lists: NIS-Elements lists: PAST lists: NVivo lists: PRISM (Stanford database) lists: Metscape lists: PROCHECK lists: oligo lists: OpenEpi lists: Pathway Commons lists: Nanoparticle Tracking Analysis lists: Openlab lists: PLINK lists: PAUP lists: NONMEM lists: PREFAB lists: NetworkX lists: PeptideProphet lists: Primer Designer lists: PhyML lists: PASS lists: PyMOL lists: PSIPRED lists: PROFILER lists: PHYLIP lists: Phobius lists: Prime lists: Phyutility lists: Picard lists: ProteinProphet lists: Phaser lists: ProSAS lists: PostgreSQL lists: Primer-BLAST lists: ProteinLynx Global Server lists: QUANTO lists: Primer Express lists: Primer3Plus lists: ProtTest lists: ProbCons lists: Primer3 lists: Poretools lists: Protein preparation Wizard lists: QmRLFS-finder lists: PicTar lists: RevMan lists: Pipeline Pilot lists: QIIME lists: PRISMA lists: REDCap lists: RAxML lists: Proteome Discoverer lists: Research Randomizer lists: SPARTAN lists: SPSS lists: RNAstructure lists: Refmac lists: QuantPrime lists: Prodigal lists: RepeatModeler lists: Ringo lists: SQLite lists: SAGE lists: Rhinoceros lists: SAMTOOLS lists: SPAdes lists: RepeatMasker lists: SEDFIT lists: STATISTICA lists: RNAhybrid lists: SlideBook lists: STRUCTURE lists: SABmark lists: SPM lists: Stata lists: RStudio lists: SciPy lists: Scion Image lists: Simulink lists: TAGGER lists: TopHat lists: SAM lists: ShortRead lists: SIFT lists: SCAN lists: SignalP lists: Scopus lists: Strelka2 lists: Trans-ABySS lists: Statgraphics Centurion lists: T-Coffee lists: Statistical Analysis System lists: TargetScan lists: UCHIME lists: Sequencher lists: SigmaStat lists: UCSC Genome Browser lists: affy lists: Taverna lists: MBF BioScience: Stereo Investigator lists: Trimmomatic lists: Vmatch lists: WFU PickAtlas lists: SigmaPlot lists: X!Tandem lists: STAR lists: TASSEL lists: SyStat lists: WEBLOGO lists: UCSF Chimera lists: TreeView lists: pheatmap lists: WinWCP lists: microRNA.org lists: glmnet lists: Phenix.refine lists: BASE lists: beadarray lists: RMS lists: lumi lists: Web of Science lists: minfi lists: geNORM lists: WU-BLAST lists: WinBUGS lists: SPP lists: tRNAscan-SE lists: WebPlotDigitizer lists: qBasePLUS lists: Matplotlib lists: TreeBASE lists: pClamp lists: TBLASTN lists: igraph lists: V3D lists: survival lists: miRanda lists: piRNABank lists: topGO lists: NGmerge lists: OMNISEC lists: NOTUNG lists: OpenBUGS lists: Optimization Toolbox lists: ProgRes Capture Pro lists: Ocular lists: Umediation lists: Nano Measurer lists: PHYLDOG lists: VSEARCH lists: WinNonlin lists: WHONET lists: ToposPro lists: Treerecs lists: Agilent Seahorse Wave lists: SimPhy lists: TomoStudio lists: Mutation Assessor lists: Stem lists: SRAMP lists: CRISPResso2 lists: geepack lists: Evalue lists: DAGitty lists: FastMulRFS lists: ggridges lists: gamm4 lists: AutoRT lists: CopyKAT lists: Inference of CRISPR Edits lists: classInt lists: ASTRAL-Pro lists: maftools lists: mitml lists: CMplot lists: MetaPSICOV lists: LaCyTools lists: MADOKA lists: Kaplan Meier Plotter lists: IntFOLD lists: ModFOLD lists: lDDT has parent organization: University of Texas at Austin; Texas; USA |
Sloan Foundation | DOI:10.1002/asi.24454 | Free, Available for download, Freely available | https://github.com/softcite/softcite_dataset_v2, https://zenodo.org/record/7995565 | SCR_024411 | Software Citation | 2026-08-29 11:28:10 | 0 | ||||||
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Splice AI Resource Report Resource Website 10+ mentions |
Splice AI (RRID:SCR_024532) | data analysis software, data processing software, software application, software resource | Software package annotates genetic variants with their predicted effect on splicing. Used to identify splice variants. | annotate genetic variants, predicted effect on splicing, identify splice variants, | Free, Available for download, Freely available | https://github.com/Illumina/SpliceAI | SCR_024532 | 2026-08-29 11:28:35 | 44 | ||||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | data acquisition software, data processing software, software application, software resource | Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, image acquisition, capture high quality images and video, | is listed by: SoftCite | Restricted | SCR_024490 | Teledyne Photometrics Ocular | 2026-08-29 11:28:35 | 4 | |||||||||
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Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | data analysis software, data processing software, software application, software resource | Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. | simulate unmeasured confounding in mediation analysis, mediation analysis, unmeasured confounding, | is listed by: SoftCite | PMID:28724417 | Free, Available for download, Freely available | SCR_024492 | 2026-08-29 11:28:12 | 1 |
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