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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CycIF.org Resource Report Resource Website 10+ mentions |
CycIF.org (RRID:SCR_016267) | CycIF.org | data or information resource, narrative resource, immunofluorescence, experimental protocol, immuno detection protocol, web page | Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence. | immunofluorescence, cyclic, cycif, data, software, single cell, numeric, dataset, intratumoural, heterogeneity | has parent organization: LINCS Data Portal | NHLBI U54 HL127365 | PMID:26399630 | Public | SCR_016267 | cycif.org | 2026-08-08 12:00:30 | 16 | ||||||
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Center for Expanded Data Annotation and Retrieval Resource Report Resource Website 1+ mentions |
Center for Expanded Data Annotation and Retrieval (RRID:SCR_016269) | CEDAR | ontology, data or information resource, controlled vocabulary, portal, organization portal | Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle. | Metadata, interface, metadata practice, analytics, metadata pathway, funded research, data repository, data collection, |
is related to: Stanford University; Stanford; California is related to: Yale University; Connecticut; USA is related to: University of Oxford; Oxford; United Kingdom has parent organization: Stanford Center for Biomedical Informatics Research is parent organization of: CEDAR Workbench |
NIAID U54 AI117925 | SCR_018150 | https://more.metadatacenter.org/ | SCR_016269 | 2026-08-08 12:00:51 | 4 | |||||||
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easyGV Resource Report Resource Website 1+ mentions |
easyGV (RRID:SCR_016260) | software resource, software application, data analysis software, data processing software | Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface. | glycaemic, glycemia, variability, gv, glucose, diabetes, excel |
has parent organization: University of Oxford; Oxford; United Kingdom is a plug in for: Microsoft Excel |
PMID:21714681 | Free for academic use, Free for non-commercial use, Available for download | SCR_016260 | 2026-08-08 12:00:30 | 5 | |||||||||
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Illumina: MiSeqDx System Resource Report Resource Website 1+ mentions |
Illumina: MiSeqDx System (RRID:SCR_016380) | instrument resource | MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes. | Illumina, Sequencing System, Instrument Equipment, USEDit, | Restricted | SCR_020137, Model_Number_MiSeqDx | SCR_016380 | MiSeqDx | 2026-08-08 12:00:31 | 2 | |||||||||
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Illumina: HiSeq X Resource Report Resource Website 50+ mentions |
Illumina: HiSeq X (RRID:SCR_016385) | instrument resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year. | Illumina, Sequencing System, Instrument Equipment, USEDit, | THIS RESOURCE IS NO LONGER IN SERVICE | Model_Number_HiSeq X, SCR_020131 | https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet-hiseq-x-ten.pdf | SCR_016385 | HiSeq X | 2026-08-08 12:00:53 | 62 | ||||||||
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Illumina: HiSeq 2500 System Resource Report Resource Website 50+ mentions |
Illumina: HiSeq 2500 System (RRID:SCR_016383) | instrument resource | High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023. | Illumina, Sequencing System, Instrument Equipment, USEDit, | works with: PySeq2500 | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016383.pdf | SCR_020123, Model_Number_HiSeq 2500 | https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq2500/hiseq-2500-system-guide-15035786-03.pdf, https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq2500/hiseq-2500-system-guide-15035786-03.pdf | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html | SCR_016383 | HiSeq 2500 | 2026-08-08 12:00:31 | 88 | ||||||
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PhenoSpD Resource Report Resource Website 1+ mentions |
PhenoSpD (RRID:SCR_016359) | PSD | software toolkit, software resource, software application, data analysis software, data processing software | Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool. | spectral, decomposition, matrice, phenotypic, correlation, estimation, multiple, testing, correction, human, phenome, genome, summary, statistic, decomposition, matrice, genomics |
is related to: University of Bristol; Bristol; United Kingdom is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016359 | Pheno Spectral Decomposition, PhenoSpD | 2026-08-08 12:00:53 | 6 | ||||||||
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Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | software toolkit, software resource, software application, data analysis software, data visualization software, data processing software | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Research Foundation SFB 992; German Epigenome Programme DEEP 01KU1216G |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-08-08 12:00:53 | 2806 | |||||||
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SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software toolkit, software resource, software application, data analysis software, data processing software | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-08-08 12:00:53 | 2 | |||||
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XLSTAT Resource Report Resource Website 100+ mentions |
XLSTAT (RRID:SCR_016299) | XLSTAT | software resource, software application, data management software, data analysis software, data visualization software, data processing software | Software for commercial data analysis and statistical software package for Microsoft Excel. | data, process, manage, analyze, visualize, graph, statistic, microsoft, excel | is related to: Microsoft Excel | Addinsoft | Commercially available, Trial available | SCR_016299 | XL STATistics | 2026-08-08 12:00:30 | 175 | |||||||
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TraCeR Resource Report Resource Website 10+ mentions |
TraCeR (RRID:SCR_016338) | software toolkit, software resource, software application, simulation software, data analysis software, data processing software | Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. | recovery, receptor, single, cell, data, computation, method, reconstruct, sequence, T lymphocyte, RNA, sequence |
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is related to: European Bioinformatics Institute |
European Research Council ; the Lister Institute for Preventative Medicine (S.A.T.) |
PMID:26950746 | Free, Available for download, Freely available | SCR_016338 | 2026-08-08 12:00:52 | 14 | ||||||||
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migec Resource Report Resource Website 10+ mentions |
migec (RRID:SCR_016337) | MIGEC | software toolkit, software resource, software application, data analysis software, data processing software | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President ; European Regional Development Fund |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-08-08 12:00:53 | 11 | |||||||
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clustree Resource Report Resource Website 100+ mentions |
clustree (RRID:SCR_016293) | software resource, software application, data analysis software, data visualization software, data processing software | Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties. | clustering, tree, visualisation, data, set, group, sample, similar, property, different, resolution, cluster | is related to: R Project for Statistical Computing | Free, Freely available, Available for download | https://github.com/lazappi/clustree | SCR_016293 | 2026-08-08 12:00:30 | 100 | |||||||||
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FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | software resource, software application, data analysis software, data processing software | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Netherlands Consortium for Systems Biology (NCSB) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | Flux Mode Calculator | 2026-08-08 12:00:52 | 1 | |||||
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FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | image analysis software, software resource, software application, data analysis software, data processing software | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | 2026-08-08 12:00:53 | 16 | |||||||||||
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star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | image analysis software, software resource, software application, alignment software, data processing software | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | NHLBI U54 HL127624; AMEDD Advanced Medical Technology Initiative ; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-08-08 12:00:52 | 1 | ||||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | software toolkit, software resource, software application, data analysis software, data processing software | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-08-08 12:00:53 | 1 | ||||||
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LungMap Resource Report Resource Website 50+ mentions |
LungMap (RRID:SCR_016347) | LungMAP | data or information resource, service resource, storage service resource, portal, data repository | Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool. | lung, data, histochemistry, structural, molecular, normal, perinatal, postnatal, development, mouse, human, repository, images, transcriptomic, proteomic, lipidomic |
is related to: RTI International is related to: University of Texas at Austin; Texas; USA is related to: University of Alabama at Birmingham; Alabama; USA is related to: Yale University; Connecticut; USA is related to: University of California at San Diego; California; USA is related to: Carnegie Mellon University; Pennsylvania; USA is related to: Lung Genome Browser |
the National Heart ; Lung ; and Blood Institute of the National Institutes of Health U01HL122638 |
PMID:28798251 | Free, Freely available | SCR_016347 | The Molecular Atlas of Lung Development Program | 2026-08-08 12:00:53 | 68 | ||||||
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Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | production service resource, software resource, software application, data analysis service, data management software, analysis service resource, service resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-08-08 12:00:55 | 2 | |||||||
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Ximmer Resource Report Resource Website 1+ mentions |
Ximmer (RRID:SCR_016427) | software resource, software application, simulation software, data analysis software, data visualization software, data processing software | Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data. | cnv, copy, number, variant, exome, targeted, sequencing, data, next, generation, genomic | is listed by: OMICtools | National Human Genome Research Institute ; National Eye Institute ; National Heart Lung and Blood Institute ; Australian National Health and Medical Research Council ; Victorian State Government |
DOI:10.1101/260927 | Open source, Free, Available for download, Freely available | https://omictools.com/ximmer-tool, http://ximmer.org | SCR_016427 | 2026-08-08 12:00:31 | 4 |
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