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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | analysis service resource, application programming interface, atlas, consortium, controlled vocabulary, data access protocol, data analysis service, data or information resource, data repository, database, expression atlas, ontology, organization portal, portal, production service resource, service resource, software resource, storage service resource | Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. | Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset |
is recommended by: National Library of Medicine has parent organization: Baylor College of Medicine; Houston; Texas has parent organization: exRNA |
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage | American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch ; NCATS UH3 TR000906; NCATS UH3 TR000943; NCI CA217685; NCI R01 CA163849; NCI R35 CA209904; NCI U19 CA179512; NHLBI K23 HL127099; NHLBI R01 HL122547; NHLBI R01 HL136685; NIA R01 AG059729; NIDA U54 DA036134; NIDDK P30 DK63720; NIGMS R25 GM056929 |
PMID:30951672 | Restricted | SCR_017221 | 2026-08-21 12:41:09 | 29 | |||||||
|
Harvard School of Public Health Microbiome Analysis Core Facility Resource Report Resource Website |
Harvard School of Public Health Microbiome Analysis Core Facility (RRID:SCR_017187) | HSPH Microbiome Analysis Core | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource | Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations. | bioinformatics, consulting, microbiome, omic, data, analysis | has parent organization: Harvard University; Cambridge; United States | Open | SCR_017187 | , HSPH, Harvard School of Public Health, Microbiome Analysis, facility, Core | 2026-08-21 12:41:18 | 0 | ||||||||
|
SeQuiLa Resource Report Resource Website 1+ mentions |
SeQuiLa (RRID:SCR_017220) | data analysis software, data processing software, software application, software resource | Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals. | genomic, intervals, querying, processing, Apache, Spark, SQL, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Warsaw University of Technology; Warsaw; Poland |
National Science Center ; Polish budget funds for science |
PMID:30428005 | Free, Available for download, Freely available | biotools:SeQuiLa-cov | http://biodatageeks.org/sequila/, https://bio.tools/SeQuiLa-cov | SCR_017220 | 2026-08-21 12:41:18 | 1 | ||||||
|
Computational Suite for Bioinformaticians and Biologists Resource Report Resource Website 1+ mentions |
Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) | CSBB | data analysis software, data processing software, software application, software resource | Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments. | analysis, sequencing, data, command, line, expression, normalization, convert | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_17554 | https://github.com/csbbcompbio | SCR_017234 | CSBB-v3.0, CSBB-v1.0, CSBB-v2.0, Computational Suite for Bioinformaticians and Biologists | 2026-08-21 12:41:19 | 6 | ||||||
|
Case Western Reserve University Cystic Fibrosis Mouse Models Core Resource Report Resource Website 1+ mentions |
Case Western Reserve University Cystic Fibrosis Mouse Models Core (RRID:SCR_017238) | CWR | biomaterial supply resource, material resource, organism supplier | Core facility for cystic fibrosis mouse strains. Services include mouse production from current strains and creation of new strains, mouse strain maintenance, tissue acquisition, genotyping and treatment of mice with IACUC approved drugs to test potential therapies. Maintains centralized database that contains breeding history, phenotypes observed and experimental records of various CF mouse strains. | RIN, Resource Information Network, cystic, fibrosis, mouse, strain, RRID Community Authority | is listed by: Resource Information Network | Case Western Reserve University School of Medicine ; Cystic Fibrosis Foundation |
Restricted | SCR_017238 | Case Western Reserve University, Cystic Fibrosis Mouse Model Core, CWR | 2026-08-21 12:41:19 | 3 | |||||||
|
T1D Exchange Biobank Resource Report Resource Website 1+ mentions |
T1D Exchange Biobank (RRID:SCR_017195) | biobank, data or information resource, material storage repository, service resource, storage service resource | Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes. | collection, biological, sample, data, clinical, diabetes |
is related to: Type 1 Diabetes Knowledge Portal has parent organization: T1D Exchange |
Type 1 diabetes, Diabetes | Restricted | SCR_017195 | 2026-08-21 12:41:07 | 2 | |||||||||
|
matemaker Resource Report Resource Website 1+ mentions |
matemaker (RRID:SCR_017199) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | Software tool to make artificial mate pairs from long sequences for scaffolding. | artificial, mate, pair, long, sequence, scaffolding, genomics, genome, assembly | Free, Available for download, Freely available | SCR_017199 | matemaker v1.0.0 | 2026-08-21 12:41:09 | 4 | ||||||||||
|
Open Ephys: Pulse Pal Resource Report Resource Website 1+ mentions |
Open Ephys: Pulse Pal (RRID:SCR_017203) | instrument resource | Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics. | instrument, generator, stimulation, voltage, puls, sequence, electrophysiology, psychophysics | McKnight Foundation ; NIMH R01 MH097061; NINDS R01 NS07553 |
DOI:10.3389/fneng.2014.00043 | Available for purchase | https://sanworks.io/shop/viewproduct?productID=1102, https://github.com/sanworks/PulsePal, https://sites.google.com/site/pulsepalwiki/specifications?authuser=0 | SCR_017203 | Pulse Pal v2 | 2026-08-21 12:41:07 | 2 | |||||||
|
VETA Resource Report Resource Website 1+ mentions |
VETA (RRID:SCR_017201) | data acquisition software, data analysis software, data processing software, data visualization software, software application, software resource | Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS. | Electromyography, transcranial, magnetic, stimulation, analysis, EMG, TMS, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCATS TR002370 | PMID:31572120 | Free, Available for download, Freely available | BioTools:VETA, biotools:VEtA | https://github.com/greenhouselab/Veta/tree/master/data, https://bio.tools/VETA, https://bio.tools/VETA, https://bio.tools/VETA | SCR_017201 | 2026-08-21 12:41:18 | 2 | ||||||
|
Agilent: G2565CA Microarray Scanner Resource Report Resource Website 1+ mentions |
Agilent: G2565CA Microarray Scanner (RRID:SCR_017206) | instrument resource | Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays. | microarray, analysis, Agilent, scanner, slide, fluorescence, intensity, nucleic, acid, sample | Available for purchase | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_017206.pdf | SCR_019384, Model_Number_2565CA | https://www.agilent.com/cs/library/usermanuals/Public/G2505-90019_ScannerC_User.pdf | https://www.chem-agilent.com/contents.php?id=1000947 | SCR_017206 | 2026-08-21 12:41:07 | 1 | |||||||
|
Rice_HxD_Recovery_Metabolomics Resource Report Resource Website 1+ mentions |
Rice_HxD_Recovery_Metabolomics (RRID:SCR_017204) | data analysis software, data processing software, data visualization software, software application, software resource, source code | Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress. | analysis, GC-MS, data, rice, sample, statistics, workflow | Free, Available for download, Freely available | SCR_017204 | 2026-08-21 12:41:18 | 1 | |||||||||||
|
BioViz3D Resource Report Resource Website 1+ mentions |
BioViz3D (RRID:SCR_017162) | data processing software, image analysis software, image reconstruction software, software application, software resource | Software for 3D reconstruction from serial slices. Used to create 3D model to analyse organs, tissues and cells, create photos and videos to help scientists in life science, biology and medicine, visualize, analyze and exploit information from serial slices and get accurate quantitative information from reconstructed 3D models. | 3D, reconstruction, serial, slice, create, model, analyze, organ, tissue, cell, photo, video, quantitative | Available for purchase | http://www.biovis3d.com/new_version_3.1.html | SCR_017162 | BioVis3D New Version 3.1 | 2026-08-21 12:41:08 | 4 | |||||||||
|
University of Oxford Computational Biology Research Group Core Facility Resource Report Resource Website |
University of Oxford Computational Biology Research Group Core Facility (RRID:SCR_017166) | CBRG | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource, training resource | Core provides bioinformatics training and analysis tools. Supports bioinformatics analysis at University of Oxford. | Bioinformatics, training, | has parent organization: University of Oxford; Oxford; United Kingdom | Restricted | SCR_017166 | , Computational Biology, CBRG, Core Facility, Oxford University, Research Group | 2026-08-21 12:41:08 | 0 | ||||||||
|
University of Cambridge Department of Plant Sciences Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Department of Plant Sciences Bioinformatics Core Facility (RRID:SCR_017164) | University of Cambridge Bioinformatics Core Facility | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource | Core provides assistance in data analysis to support members of Plant Sciences. | bioinformatics, data, analysis, service | has parent organization: University of Cambridge; Cambridge; United Kingdom | SCR_017164 | Department of Plant Sciences, Core Facility, Bioinformatics, University of Cambridge | 2026-08-21 12:41:17 | 0 | |||||||||
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UCSF Gladstone Institutes Bioinformatics Core Facility Resource Report Resource Website |
UCSF Gladstone Institutes Bioinformatics Core Facility (RRID:SCR_017178) | UCSF Gladstone Institutes Bioinformatics Core | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource, software resource, training service resource | Core provides consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools. | Bioinformatics, consulting, data, analysis, sequencing, RNA-seq, DNA-seq, ChIP-seq, ATAC-seq, statistics, variant, calling, normalization | Open | SCR_017178 | Bioinformatics Core, Gladstone Core Services, University California San Fransisco, UCSF, Gladstone Institutes | 2026-08-21 12:41:08 | 0 | |||||||||
|
Bonsai Resource Report Resource Website 100+ mentions |
Bonsai (RRID:SCR_017218) | data acquisition software, data processing software, software application, software resource | Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world. | Event, based, framework, processing, controlling, data, stream | Bial Foundation ; Champalimaud Foundation ; European Union Seventh Framework Programme ; Foundation for Science and Technology |
PMID:25904861 | Free, Available for download, Freely available | https://github.com/bonsai-rx/bonsai-rx.github.io | SCR_017218 | 2026-08-21 12:41:09 | 105 | ||||||||
|
RNAstructure Resource Report Resource Website 50+ mentions |
RNAstructure (RRID:SCR_017216) | analysis service resource, data access protocol, production service resource, service resource, simulation software, software application, software resource, web service | Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. | RNA, DNA, secondary, structure, prediction, analysis |
is listed by: SoftCite has parent organization: University of Rochester; New York; USA |
NIGMS R01 GM076485 | PMID:23620284 | Free, Freely available | SCR_017216 | 2026-08-21 12:41:07 | 58 | ||||||||
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University of Manchester Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) | Manchester Bioinformatics Facility | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource, software resource | Core provides assistance in integrative analysis of genomic datasets to support faculty. | bioinformatics, analysis, genomic, data, dataset | has parent organization: University of Manchester; Manchester; United Kingdom | Restricted | SCR_017171 | , Bioinformatics Facility, University of Manchester, Bioinformatics Core Facility | 2026-08-21 12:41:17 | 2 | ||||||||
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Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany Resource Report Resource Website |
Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany (RRID:SCR_017170) | data or information resource, organization, portal, topical portal | Interdisciplinary research institute that conducts basic research in modern immunobiology, developmental biology and epigenetics. | Institution, immunobiology, developmental, biology, epigenetics, research, Germany | is parent organization of: Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility | Wikidata Q1912076, GRID grid.429509.3, ISNI 0000 0004 0491 4256 | https://ror.org/058xzat49 | SCR_017170 | 2026-08-21 12:41:08 | 0 | |||||||||
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PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | data analysis software, data processing software, software application, software resource | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-08-21 12:41:18 | 19 |
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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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