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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Multi Gauge Resource Report Resource Website 10+ mentions |
Multi Gauge (RRID:SCR_014299) | data analysis software, software resource, data processing software, software application | A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series. | data analysis software, one dimensional electrophoretic analysis, fluorophore, multi channel fluorescence data | is listed by: SoftCite | http://www.scienceimaging.se/application-info/55.html | SCR_014299 | MultiGuage | 2026-02-13 10:57:17 | 36 | |||||||||
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Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | data visualization software, data processing software, data analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | OriginPro | 2026-02-13 10:57:14 | 13956 | |||||||
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Refmac Resource Report Resource Website 1000+ mentions |
Refmac (RRID:SCR_014225) | sequence analysis software, data processing software, data analysis software, software application, software resource | A molecular refinement program with two main modes: REVIEW, which checks and updates the input model to establish that the geometric restraints can be properly set up, and REFINE mode, which is the standard mode and documented in keywords. In REVIEW users can: check model coordinates and write an extended output set of coordinates, find disulphide bonds and other covalent links, cis-peptides, output the sequence and REMARK records. In REFINEMENT mode users can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. Also in REFINEMENT mode, Refmac produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps. The program is supported by CCP4. | molecular refinement, data analysis software, sequence analysis software |
is used by: PDB-REDO is listed by: SoftCite |
SCR_014225 | 2026-02-13 10:57:16 | 1978 | |||||||||||
|
Phenix Resource Report Resource Website 10000+ mentions |
Phenix (RRID:SCR_014224) | data processing software, software application, software resource, image reconstruction software, image analysis software | A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab. | automation, molecular structure, xray crystallography, neutron crystallography, image reconstruction software |
is listed by: SoftCite is affiliated with: Phaser is related to: MolProbity has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at Berkeley; Berkeley; USA provides: Phenix.refine |
NIGMS | Available for download, Free for nonprofit work, Acknowledgement requested, For profit groups may access PHENIX through a Consortium agreement | https://www.phenix-online.org/documentation/ | SCR_014224 | Python-based Hierarchical ENvironment for Integrated Xtallography | 2026-02-13 10:57:15 | 10587 | |||||||
|
Clocklab Resource Report Resource Website 500+ mentions |
Clocklab (RRID:SCR_014309) | data processing software, data acquisition software, data analysis software, software application, software resource, standalone software | Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program. | circadian activity data, interactive, data analysis software, data acquisition software, standalone software | is listed by: SoftCite | Pay for product, Users can order different components of ClockLab separately | SCR_014309 | 2026-02-13 10:57:17 | 546 | ||||||||||
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LabView Resource Report Resource Website 100+ mentions |
LabView (RRID:SCR_014325) | software development environment, software resource, software application, software development tool | A development environment for engineers and scientists to visualize, create, and code engineering systems. The system design software is integrated with all measurement hardware and contains signal processing IP. Other features include multithreaded execution, software deployment to hardware, and program integration into a single environment. | development environment, system design software, software development tool |
is used by: Demon Voltammetry and Analysis Software is listed by: SoftCite is related to: ZebEyeTrack is related to: ActiView |
Pay for product, Free trail is available | SCR_014325 | LabVIEW System Design Software, NI LabVIEW software, LabView System Design Software, LabVIEW | 2026-02-13 10:57:18 | 244 | |||||||||
|
Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | data processing software, software application, software resource, signal processing software, standalone software | A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters. | server, software package, mass spectrometry, protein, identify, characterize, bio.tools |
is used by: MSQuant is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MascotScan |
Free, Can be licensed for in-house use, Available for download | biotools:MASCOT | http://www.matrixscience.com/search_intro.html https://bio.tools/MASCOT |
SCR_014322 | Mascot Server | 2026-02-13 10:57:16 | 6896 | |||||||
|
PAST Resource Report Resource Website 100+ mentions |
PAST (RRID:SCR_019129) | data analysis software, software resource, data processing software, software application | Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy. | Paleontological statistics, data analysis, data manipulation function, data plotting, multivariate statistics, ecological analysis, spatial analysis, morphometrics, stratography | is listed by: SoftCite | Free, Available for download, Freely available | SCR_019129 | PAST 4.03, PAleontological STatistics | 2026-02-13 10:58:21 | 123 | |||||||||
|
MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | data processing software, data analysis software, data analytics software, software application, software resource | Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. | Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide |
uses: Mascot is listed by: SoftCite |
Free, Available for download | http://msquant.alwaysdata.net/ | SCR_019206 | 2026-02-13 10:58:20 | 4 | |||||||||
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biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, software resource, data processing software, software application | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-02-13 10:58:23 | 2638 | ||||||
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Epi Info Resource Report Resource Website 10+ mentions |
Epi Info (RRID:SCR_021682) | data processing software, data analysis software, data analytics software, software toolkit, software application, software resource | Software suite of interoperable software tools designed for global community of public health practitioners and researchers. Provides easy data entry form and database construction, customized data entry experience, and data analysis with epidemiologic statistics, maps, and graphs for public health professionals who may lack information technology background.Statistical software for epidemiology developed by Centers for Disease Control and Prevention in Atlanta, Georgia. Available for Microsoft Windows, Android and iOS, along with web and cloud version. | Centers for Disease Control and Prevention, data analysis, epidemiologic statistics, maps, graphs, public health professionals tools | is listed by: SoftCite | Free, Available for download, Freely available | SCR_021682 | Epi Info TM, Epi Info™, Epi Info 6, Epi Info 7 | 2026-02-13 10:58:37 | 24 | |||||||||
|
FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | sequence analysis software, data processing software, data analysis software, software application, software resource | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873; NHGRI R01 HG006677 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/ https://bio.tools/flash https://sources.debian.org/src/flash/ |
SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-02-13 10:55:38 | 2175 | ||||
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RAxML Resource Report Resource Website 10000+ mentions |
RAxML (RRID:SCR_006086) | RAxML | data analysis software, software resource, data processing software, software application | Software program for phylogenetic analyses of large datasets under maximum likelihood. | phylogeny, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: RAxML Next Generation works with: PAML |
PMID:24451623 PMID:16928733 PMID:15608047 DOI:10.1093/bioinformatics/btu033 |
GNU General Public License | biotools:raxml, OMICS_02242 | https://bio.tools/raxml https://sources.debian.org/src/raxml/ |
SCR_006086 | Randomized Axelerated Maximum Likelihood | 2026-02-13 10:55:45 | 12473 | |||||
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Galaxy Resource Report Resource Website 5000+ mentions |
Galaxy (RRID:SCR_006281) | Galaxy | data analysis service, portal, analysis service resource, data or information resource, production service resource, organization portal, service resource | Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases. | bioinformatics, workflow, analysis, data sharing, visualization, cloud, genomics, metagenomics, next-generation sequencing, platform, data set, genaddiction tool |
is used by: Nebula lists: PathwayMatcher is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: SoftCite is related to: ABrowse is related to: TRAMS is related to: Stem Cell Commons is related to: Stem Cell Discovery Engine is related to: CardioVascular Research Grid (CVRG) is related to: rQuant is related to: SnpEff is related to: Binding and Expression Target Analysis is related to: PIPE-CLIP is related to: Stem Cell Discovery Engine is related to: Computational Genomics Analysis Tools is related to: SpliceTrap is related to: SMAGEXP is related to: CandiMeth is related to: ewas-galaxy is related to: CLIP-Explorer is related to: Galactic Circos is related to: Tool recommender system in Galaxy is related to: NanoGalaxy is related to: Cistrome is related to: Training Infrastructure as a Service has parent organization: Pennsylvania State University is parent organization of: kmer-SVM works with: Deeptools |
Huck Institutes for the Life Sciences ; Pennsylvania Department of Health ; NSF DBI0850103; NHGRI HG004909; NHGRI HG005133; NHGRI HG005542; Institute for CyberScience at Pennsylvania State University ; Pennsylvania ; USA ; Johns Hopkins University |
PMID:20738864 PMID:20069535 PMID:16169926 |
Free, Freely available | nlx_151896, OMICS_01141 | https://usegalaxy.org/ https://sources.debian.org/src/galaxy/ |
SCR_006281 | The Galaxy Project, Galaxy Project | 2026-02-13 10:55:49 | 5473 | ||||
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OMTools Resource Report Resource Website 1+ mentions |
OMTools (RRID:SCR_017143) | data visualization software, data processing software, alignment software, data analysis software, software toolkit, software application, software resource, image analysis software | Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles. | optical, mapping, data, processing, analysis, visualization, large, scale, profile, phylogenesis | is listed by: SoftCite | Food and Health Bureau of the Hong Kong Special Administrative Region ; Chinese University of Hong Kong ; HKSAR Research Grants Council ; Lo Kwee-Seong Biomedical Research Fund ; Lee Hysan Foundation |
PMID:28505226 | Free, Available for download, Freely available | SCR_017143 | 2026-02-13 10:57:57 | 2 | ||||||||
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DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software 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 | 2026-02-13 10:57:55 | 366 | ||||
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MUMmer Resource Report Resource Website 100+ mentions |
MUMmer (RRID:SCR_018171) | data processing software, alignment software, software application, software resource, image analysis software | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer https://bio.tools/mummer https://sources.debian.org/src/mummer/ |
SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-02-13 10:58:08 | 480 | |||||
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WinBUGS Resource Report Resource Website 100+ mentions |
WinBUGS (RRID:SCR_018516) | data analysis software, software resource, data processing software, software application | Software package for Bayesian analysis of complex statistical models using Markov chain Monte Carlo methods. | Bayesian analysis, statistical model analysis, Markov chain Monte Carlo, data analysis |
is listed by: SoftCite has parent organization: University of Cambridge; Cambridge; United Kingdom |
Restricted | SCR_018516 | Win Bayesian inference Using Gibbs Sampling | 2026-02-13 10:58:13 | 215 | |||||||||
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Vmatch Resource Report Resource Website 10+ mentions |
Vmatch (RRID:SCR_018968) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch https://sources.debian.org/src/vmatch/ |
SCR_018968 | 2026-02-13 10:58:18 | 35 | ||||||||
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Leica QWin Resource Report Resource Website 1+ mentions |
Leica QWin (RRID:SCR_018940) | data processing software, software application, image processing software, software resource, image analysis software | Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional. | Leica, microscope, digital camera, image analysis, image processing, quantitative microscopy | is listed by: SoftCite | Restricted | http://www.mcbainsystems.com/pdf/Leica_QWin.pdf | SCR_018940 | 2026-02-13 10:58:23 | 4 |
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