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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NHGRI R01 HG010040; NSFC |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg, https://sources.debian.org/src/wtdbg2/ | SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-09-03 04:54:30 | 66 | |||||
|
PSMC Resource Report Resource Website 10+ mentions |
PSMC (RRID:SCR_017229) | data analysis software, data processing software, software application, software resource | Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence. | pairwise, sequentially, Markovian, coalescent, model, infer, population, size, history, diploid, sequence | Free, Available for download, Freely available | SCR_017229 | Pairwise Sequentially Markovian Coalescent | 2026-09-03 04:54:23 | 17 | ||||||||||
|
prank Resource Report Resource Website 100+ mentions |
prank (RRID:SCR_017228) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences. | multiple, nucleotide, sequence, alignment, DNA, codon, amino acid, phylogenetic, gap, predict, location, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:24170401 PMID:21110866 |
Free, Available for download, Freely available | biotools:prank, SCR_024174, OMICS_12425 | https://www.ebi.ac.uk/goldman-srv/webprank/, https://ariloytynoja.github.io/prank-msa/, https://bio.tools/prank | https://omictools.com/prank-tool | SCR_017228 | PRANK | 2026-09-03 04:54:19 | 281 | |||||
|
3D de novo assembly Resource Report Resource Website 10+ mentions |
3D de novo assembly (RRID:SCR_017227) | data analysis software, data processing software, software application, software resource | Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly. | de novo, assembly, 3D, DNA, HI-C, data, scaffold, pipeline, chromosome, genome | DOI:10.1126/science.aal3327 | Free, Available for download, Freely available | SCR_017227 | 2026-09-03 04:54:25 | 42 | ||||||||||
|
University of North Carolina Charlotte Bioinformatics Services Division Resource Report Resource Website |
University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) | BiSD, UNC Charlotte BiSD | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource | Core to assist with analyzing and interpreting data produced by genomic technologies. | bioinformatics, analysis, data, genomic | Open | SCR_017182 | , Charlotte, University of North Carolina, BiSD, Bioinformatics Services Division, UNC | 2026-09-03 04:54:17 | 0 | |||||||||
|
Carnegie Institution for Science Department Washington of Embryology Core Facility Resource Report Resource Website |
Carnegie Institution for Science Department Washington of Embryology Core Facility (RRID:SCR_017181) | GRACE | access service resource, service resource, data or information resource, core facility, training service resource | Provide tools for research study in genetics, biochemistry, proteomics, and genomics. | bioinformatics, genetics, biochemistry, proteomics, genomics | was submitted by: Resource Identification Portal | Restricted | SCR_017181 | Carnegie Institution for Science, Core Facility, Genomic Resources At Carnegie Embryology, Department of Embryology, GRACE | 2026-09-03 04:54:21 | 0 | ||||||||
|
City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) | IGBC | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource | Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators. | bioinformatics, genomic, data, analysis, service, next, sequencing | Restricted | SCR_017188 | , City of Hope, Integrative Genomics and Bioinformatics Core, Bioinformatics Core Facility, National Medical Center, IGBC | 2026-09-03 04:54:19 | 1 | |||||||||
|
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 | 2026-09-03 04:54:13 | 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 | 2026-09-03 04:54:09 | 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 | 2026-09-03 04:54:23 | 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 | 2026-09-03 04:54:14 | 6 | ||||||
|
Scanco: Medical microCT 100 system Resource Report Resource Website 1+ mentions |
Scanco: Medical microCT 100 system (RRID:SCR_017119) | instrument resource | Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG. | SCANCO, micro, CT, computed, tomography, scanner, 3D, imaging, speciment, in vitro, analysis, visualization, image, data | Available for purchase | https://www.scanco.ch/images/Brochures/microct-v16.pdf | http://www.scanco.ch/en/systems-solutions/specimen/microct100.html | SCR_017119 | 2026-09-03 04:54:12 | 7 | |||||||||
|
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 | 2026-09-03 04:54:25 | 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 | 2026-09-03 04:54:22 | 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 | 2026-09-03 04:54:21 | 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 | 2026-09-03 04:54:21 | 2 | |||||||
|
Keyence: BZ X-710 fluorescent microscope Resource Report Resource Website 10+ mentions |
Keyence: BZ X-710 fluorescent microscope (RRID:SCR_017202) | instrument resource | All in one fluorescence microscope BZ-X710 by Keyence, Japan. | instrument, fluorescence, microscope, Keyence | Available for purchase | https://www.keyence.com/products/microscope/fluorescence-microscope/bz-x700/models/bz-x710/ | SCR_017202 | 2026-09-03 04:54:18 | 25 | ||||||||||
|
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 | 2026-09-03 04:54:29 | 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 | 2026-09-03 04:54:22 | 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 | 2026-09-03 04:54:22 | 1 |
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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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