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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) | database, production service resource, data repository, storage service resource, data analysis service, portal, controlled vocabulary, consortium, data or information resource, data access protocol, ontology, analysis service resource, software resource, application programming interface, expression atlas, atlas, service resource, organization portal | 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 | NIDA U54 DA036134; NCI R01 CA163849; NIGMS R25 GM056929; NCATS UH3 TR000906; NCI U19 CA179512; NIDDK P30 DK63720; NHLBI K23 HL127099; NHLBI R01 HL136685; NIA R01 AG059729; NCATS UH3 TR000943; NCI R35 CA209904; NCI CA217685; NHLBI R01 HL122547; American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch |
PMID:30951672 | Restricted | SCR_017221 | 2026-08-14 09:28:01 | 29 | |||||||
|
Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | data processing software, software application, data analysis software, software resource | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-08-14 09:27:36 | 16 | |||||||||
|
SeQuiLa Resource Report Resource Website 1+ mentions |
SeQuiLa (RRID:SCR_017220) | data processing software, software application, data analysis software, 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 | 2026-08-14 09:27:34 | 1 | ||||||
|
Horos Resource Report Resource Website 10+ mentions |
Horos (RRID:SCR_017340) | data processing software, data visualization software, software application, software resource | Software tool as open source medical image viewer. Enables to browse and visualize medical imaging libraries. | Medical, image, viewer, ivisualize, medical, imaging, library | Restricted | SCR_017340 | 2026-08-14 09:28:04 | 14 | |||||||||||
|
miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | database, web service, data or information resource, data access protocol, software resource | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-08-14 09:27:45 | 73 | ||||||
|
Computational Suite for Bioinformaticians and Biologists Resource Report Resource Website 1+ mentions |
Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) | CSBB | data processing software, software application, data analysis software, 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 | 2026-08-14 09:27:34 | 6 | ||||||
|
fastMNN Resource Report Resource Website 1+ mentions |
fastMNN (RRID:SCR_017351) | data processing software, software application, data analysis software, software resource | Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method. | Correct, batch, effect, single, cell, expression, data, fast, version, mutual, nearest, neighbors | Free, Available for download, Freely available | SCR_017351 | Fast Mutual Nearest Neighbors | 2026-08-14 09:28:04 | 9 | ||||||||||
|
SleepTrip Resource Report Resource Website 10+ mentions |
SleepTrip (RRID:SCR_017318) | data processing software, software application, data analysis software, software resource | Software as branch of FieldTrip with added functionality for sleep analyses, like calculating sleep tables, descriptives, ploting hypnograms, detecting slow waves, sleep spindles, REMS and their cooccurrence etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | slow, wave, oscillation, spindle, cooccurrence, rapid, eye, movements, sleep table, hypnogram |
is related to: SpiSOP works with: FieldTrip |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/Frederik-D-Weber/sleeptrip | SCR_017318 | SpiSOP | 2026-08-14 09:27:35 | 16 | ||||||||
|
GraphClust2 Resource Report Resource Website 1+ mentions |
GraphClust2 (RRID:SCR_017286) | data processing software, web application, software application, data analysis software, software resource | Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function. | scalable, clustering, RNA, sequence, secondary, structure, function, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
German Research Foundation Collaborative Research Centre 992 Medical Epigenetics ; German Federal Ministry of Education and Research |
PMID:31808801 PMID:22689765 |
Free, Available for download, Freely available | biotools:GraphClust2 | https://bio.tools/GraphClust2 | SCR_017286 | GraphClust, GraphClust-2 | 2026-08-14 09:27:35 | 4 | |||||
|
redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | production service resource, data processing software, data analysis service, software application, data analysis software, software resource, service resource, analysis service resource | Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data. | microbiome, feature, identify, characterize, analysis, metadata, sample, data | PMID:31239397 | Free, Available for download, Freely available | SCR_017285 | 2026-08-14 09:27:44 | 5 | ||||||||||
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PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data processing software, software application, data analysis software, software resource | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-08-14 09:27:36 | 15 | ||||||||
|
Bonsai Resource Report Resource Website 100+ mentions |
Bonsai (RRID:SCR_017218) | data processing software, software application, software resource, data acquisition software | 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 | European Union Seventh Framework Programme ; Bial Foundation ; Foundation for Science and Technology ; Champalimaud Foundation |
PMID:25904861 | Free, Available for download, Freely available | https://github.com/bonsai-rx/bonsai-rx.github.io | SCR_017218 | 2026-08-14 09:28:00 | 105 | ||||||||
|
RNAstructure Resource Report Resource Website 50+ mentions |
RNAstructure (RRID:SCR_017216) | simulation software, production service resource, web service, data access protocol, software application, software resource, service resource, analysis service resource | 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 | 2026-08-14 09:27:43 | 58 | ||||||||
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Excel Statistics Resource Report Resource Website 10+ mentions |
Excel Statistics (RRID:SCR_017294) | software toolkit, software application, data analytics software, software resource | Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu . | statistical, analysis, BellCurve, Excell | Restricted | SCR_017294 | 2026-08-14 09:28:02 | 29 | |||||||||||
|
SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | data processing software, software application, software resource, data acquisition software | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-08-14 09:27:35 | 228 | |||||||||
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PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | data processing software, software application, data analysis software, 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 | 2026-08-14 09:27:43 | 19 | ||||||
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TWOSEX-MSChart Resource Report Resource Website 10+ mentions |
TWOSEX-MSChart (RRID:SCR_017298) | data processing software, software application, data analysis software, software resource | Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan. | life, table, analysis, development, cohort, population, animal, species, sex | Restricted | SCR_017298 | 2026-08-14 09:28:02 | 14 | |||||||||||
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Proovread Resource Report Resource Website 10+ mentions |
Proovread (RRID:SCR_017331) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool for PacBio hybrid error correction through iterative short read consensus. | PacBio, hybrid, error, correction, short, read, consensus, DNA, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BWA is related to: BLASR is related to: SHRiMP |
European Research Council | PMID:25015988 | Free, Available for download, Freely available | biotools:proovread | https://bio.tools/proovread | SCR_017331 | 2026-08-14 09:28:03 | 14 | ||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | production service resource, data analysis service, controlled vocabulary, ontology, data or information resource, service resource, analysis service resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-08-14 09:27:36 | 187 | |||||||
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Protomo Resource Report Resource Website 1+ mentions |
Protomo (RRID:SCR_017296) | data processing software, software application, image processing software, software resource | Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler. | electron, tomography, 3D, image, processing | NIGMS GM30598; NIGMS GM64346 |
PMID:16973379 | Restricted | SCR_017296 | 2026-08-14 09:27:35 | 5 |
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