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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | software application, software resource, data analysis software, data processing software | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | NIH Office of the Director DP2 OD008540; NHLBI U01 HL130010; NSF PHY-1427654; NHGRI HG006193; Welch Foundation ; Cancer Prevention Research Institute of Texas ; NVIDIA Research Center Award ; IBM University Challenge Award ; Google Research Award ; McNair Medical Institute Scholar Award ; President Early Career Award in Science and Engineering ; NHGRI HG003067; PD Soros Fellowship |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-07-28 09:44:31 | 108 | ||||||||
|
DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
European Social Fund ; John S. Latsis Public Benefit Foundation ; Development Grants For Research Institutions – KRIPIS ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; European Regional Development Fund |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/, http://www.microrna.gr/miRPathv3, https://bio.tools/diana-mirpath | http://www.microrna.gr/miRPathv2 | SCR_017354 | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-07-28 09:44:33 | 366 | ||||
|
PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-07-28 09:44:29 | 7 | ||||||||
|
Relacs Resource Report Resource Website 1+ mentions |
Relacs (RRID:SCR_017280) | software application, data analysis software, software resource, data processing software, data acquisition software | Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings. | data, acquisition, analysis, electrophysiology, neuronal, response, control, stimulation | Free, Available for download, Freely available | SCR_017280 | Control, and Stimulation, Relaxed Electrophysiological Data Acquisition | 2026-07-28 09:44:32 | 2 | ||||||||||
|
Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | software application, data analysis software, software resource, data processing software, data visualization software, segmentation software, 3d visualization software, image analysis software | Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience. | MBF Bioscience, vasculature, reconstruction, image, analysis, 3D, vessel, data, automatic, quantify, anastomoses, microvascular |
is used by: SPARC Portal works with: Vesselucida Explorer |
Restrcited | https://learn.mbfbioscience.com/vle.html | SCR_017320 | Vesselucida 360, Vesselucida | 2026-07-28 09:44:33 | 2 | |||||||
|
trimAl Resource Report Resource Website 500+ mentions |
trimAl (RRID:SCR_017334) | software application, software resource, data analysis software, data processing software | Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses. | removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
FIS ; MEC |
PMID:19505945 | Free, Available for download, Freely available | biotools:trimal | https://vicfero.github.io/trimal/, https://bio.tools/trimal | SCR_017334 | 2026-07-28 09:44:29 | 582 | ||||||
|
GCE Resource Report Resource Website 10+ mentions |
GCE (RRID:SCR_017332) | software application, software resource, data analysis software, data processing software | Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics. | estimation, genomic, characteristic, analysis, k-mer, frequencey, de novo | ftp://ftp.genomics.org.cn/pub/gce | SCR_017332 | Genomic Characteristics Estimation | 2026-07-28 09:44:33 | 14 | ||||||||||
|
MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | software application, software resource, data analysis software, data processing software | Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab. | post, process, magnetic, resonance, spectroscopy, data, analysis |
has parent organization: University of Minnesota Twin Cities; Minnesota; USA works with: MATLAB |
Restricted | SCR_017292 | Magnetic Resonance signal processing and analysis | 2026-07-28 09:44:28 | 19 | |||||||||
|
IKAP Resource Report Resource Website 1+ mentions |
IKAP (RRID:SCR_017417) | software application, software resource, data analysis software, data processing software | Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation. | Identify, cell, population, group, single, cell, RNAseq, analysis, clustering, dataset | DOI:10.1101/596817 | Free, Available for download, Freely available | SCR_017417 | Identifying K mAjor cell Population | 2026-07-28 09:44:35 | 2 | |||||||||
|
Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | software application, data analysis software, software resource, data processing software, data visualization software | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Viertel Fellowship ; Victorian State Government Operational Infrastructure Support and Australian Government |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-07-28 09:44:29 | 23 | ||||||||
|
The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | software application, software resource, data analysis software, data processing software | Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data. | Multivariate, analysis, structural, MRI, data, functional, imaging, brain | German Ministry of Education and Research ; German Research Foundation |
PMID:25610393 | Free, Available for download, Freely available | SCR_017424 | 2026-07-28 09:44:34 | 13 | ||||||||
|
BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
Royal Society of New Zealand Marsden award ; European Research Council ; NIGMS U01 GM110749; Swiss National Science foundation ; Max Planck Society ; EMBL |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-07-28 09:44:33 | 194 | |||||||
|
SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-07-28 09:44:32 | 2 | |||||||||
|
QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | software application, software resource, data analysis software, data processing software | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-07-28 09:44:29 | 28 | |||||||||||
|
SCÅTTER Resource Report Resource Website 50+ mentions |
SCÅTTER (RRID:SCR_017271) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets. | analysis, data, dataset, small, angle, X ray, scattering, SAXS, BIOISIS | Department of Energy Office of Science Integrated Diffraction Analysis Technologies ; National Cancer Institute Structural Cell Biology of DNA Repair Machines ; National Institute of General Medical Sciences project MINOS |
Restricted | https://bl1231.als.lbl.gov/scatter/ | SCR_017271 | 2026-07-28 09:44:32 | 84 | |||||||||
|
Cancer Dependency Map Portal Resource Report Resource Website 1000+ mentions |
Cancer Dependency Map Portal (RRID:SCR_017655) | DepMap Portal | data set, project portal, data or information resource, catalog, database, portal | Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication. | Cancer, vulnerability, dataset, visualization, analysis, tool, catalog, biomarker, genetic, drug, sensitivity, tumor, model, FASEB list | has parent organization: Broad Institute | Free, Available for download, Freely available | SCR_017655 | Dependency Map Portal, Dependency Map portal, Cancer DepMap, Cancer Dependency Map Project | 2026-07-28 09:44:39 | 1000 | ||||||||
|
Deep Blue Epigenomic Data Server Resource Report Resource Website 1+ mentions |
Deep Blue Epigenomic Data Server (RRID:SCR_017490) | service resource, data or information resource, data access protocol, software resource, web service, access service resource | Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis. | Data, epigenomic, collection, ontology, storing, distributing, organizing, retriving, searching, genetic, metadata, analysis |
uses: ENCODE uses: Blueprint Epigenome uses: NIH Roadmap is related to: Roadmap Epigenomics Project |
German Science Ministry ; EU |
Free, Freely available | SCR_017490 | 2026-07-28 09:44:36 | 2 | |||||||||
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iBright Analysis Software Resource Report Resource Website 10+ mentions |
iBright Analysis Software (RRID:SCR_017632) | software application, data analysis software, software resource, data processing software, image analysis software | Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform. | Invitrogen, image, adjustment, data, analysis, blot, gel, iBright Imaging System | Free, Available for download, Freely available | SCR_017632 | 2026-07-28 09:44:35 | 17 | |||||||||||
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Batch Data and Analysis Tool Resource Report Resource Website 1+ mentions |
Batch Data and Analysis Tool (RRID:SCR_017515) | data or information resource, service resource | Software tool to access various mouse genome information in batch format. Batch data and analysis tools. | Mouse, genome, information, batch, format, data, analysis, tool | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017515 | 2026-07-28 09:44:37 | 3 | ||||||||||
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RAMPAGE Resource Report Resource Website 100+ mentions |
RAMPAGE (RRID:SCR_017590) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure. | Ramachandran, plot, analysis, upload, PDB, file, coputing, dihedral, angle, extracting, sequence, protein, amino acid, residue, structure | has parent organization: University of Cambridge; Cambridge; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_017590 | 2026-07-28 09:44:31 | 124 |
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