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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TargetScan Resource Report Resource Website 10000+ mentions |
TargetScan (RRID:SCR_010845) | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals. | predict, biological, target, miRNA, conserved, 8mer, 7mer, site, match seed, region, nonconserved, mismatched, pair |
is listed by: OMICtools is listed by: SoftCite has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NIGMS GM067031; Howard Hughes Medical Institute ; NSF Graduate Research Fellowship |
PMID:26267216 | Free, Freely available | OMICS_00420 | http://www.targetscan.org/vert_71/ | SCR_010845 | TargetScanFly | 2026-02-14 02:01:50 | 10783 | |||||
|
CEAS Resource Report Resource Website 100+ mentions |
CEAS (RRID:SCR_010946) | CEAS | software resource | Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00802 | SCR_010946 | 2026-02-14 02:02:07 | 397 | |||||||||
|
NIA Array Analysis Resource Report Resource Website 10+ mentions |
NIA Array Analysis (RRID:SCR_010948) | NIA Array Analysis | data analysis service, analysis service resource, data set, data or information resource, production service resource, service resource, software resource | Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available. | gene expression, microarray, principal component analysis, significance analysis, gene annotation, anova, hierarchical clustering, pattern matching |
is listed by: OMICtools is listed by: SoftCite has parent organization: National Institute on Aging |
PMID:15734774 | OMICS_00774 | SCR_010948 | 2026-02-14 02:01:52 | 48 | ||||||||
|
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 | 2026-02-14 02:03:34 | 480 | |||||
|
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 | 2026-02-14 02:03:21 | 215 | |||||||||
|
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 | 2026-02-14 02:03:43 | 35 | ||||||||
|
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 | 2026-02-14 02:03:43 | 4 | |||||||||
|
SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | web service, data analysis service, analysis service resource, production service resource, source code, service resource, data access protocol, software resource | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/ https://bio.tools/sift https://sources.debian.org/src/sift/ |
http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-02-14 02:02:17 | 10223 | |||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-02-14 02:02:16 | 318 | ||||||||
|
Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-02-14 02:02:45 | 38 | ||||||||||
|
MPlus Resource Report Resource Website 500+ mentions |
MPlus (RRID:SCR_015578) | data processing software, data analysis software, software application, software resource, simulation software | Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data. | statistical modeling software, data imaging software, software model, modeling estimator, modeling algorithms | is listed by: SoftCite | Available for purchase, Free demo available, Student pricing is available | SCR_015578 | Mplus Version 8 | 2026-02-14 02:03:06 | 958 | |||||||||
|
MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canadian Institutes for Health Research ; Genome Alberta ; McGill University ; Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-02-14 02:03:03 | 10983 | |||||
|
X!Tandem Resource Report Resource Website 10+ mentions |
X!Tandem (RRID:SCR_015645) | data analysis software, software resource, data processing software, software application | Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences. | Search engine, command line tool, matching tandem mass spectra, peptide sequence, protein sequence, protein identification, tandem mass spectrum, xml file, FASEB list |
is listed by: SoftCite is related to: XTandem Parser |
Free, Available for download, Freely available | SCR_018388 | SCR_015645 | 2026-02-14 02:02:52 | 44 | |||||||||
|
JASP Resource Report Resource Website 1000+ mentions |
JASP (RRID:SCR_015823) | data analysis software, software resource, data processing software, software application | Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests. | statistical analysis, data analysis, statistical test, frequentist analysis, bayesian analysis, r package |
uses: R Project for Statistical Computing is listed by: SoftCite |
European Research Council | PMID:28685272 | Open source, Free, Available for download, Tutorial available, Runs on Windows, Runs on MAC OS, Runs on Linux | https://github.com/jasp-stats/jasp-desktop | SCR_015823 | 2026-02-14 02:02:55 | 3851 | |||||||
|
MCODE Resource Report Resource Website 1000+ mentions |
MCODE (RRID:SCR_015828) | data processing software, image analysis software, data analysis software, software application, software resource, algorithm resource | Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks. | cluster, clustering, graph analysis, network, network topology, interconnectivity | is listed by: SoftCite | Canadian Institutes of Health Research (CIHR) ; Ontario Research and Development Challenge Fund ; MDS-Sciex |
PMID:12525261 PMID:25570063 |
Free, Available for download | http://baderlab.org/Software/MCODE | SCR_015828 | 2026-02-14 02:02:55 | 1150 | |||||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | sequence analysis software, data processing software, data analysis software, software toolkit, software application, software resource | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-02-14 02:03:06 | 81 | ||||||
|
Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data processing software, data analysis software, software application, software resource, simulation software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-02-14 02:02:56 | 1146 | ||||||
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CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | software resource, data analysis software, data processing software, software application | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-02-14 02:01:40 | 413 | ||||
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SigmaStat Resource Report Resource Website 5000+ mentions |
SigmaStat (RRID:SCR_010285) | SigmaPlot, SigmaStat | data visualization software, data processing software, portal, data or information resource, organization portal, software application, software resource | Software tool for data graphing and analysis by Systat Software, Inc. | is listed by: SoftCite | Commercially available, Free trial available | nlx_157306 | SCR_010285 | SigmaPlot, SigmaStat | 2026-02-14 02:01:56 | 7161 | ||||||||
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PSIPRED Resource Report Resource Website 1000+ mentions |
PSIPRED (RRID:SCR_010246) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences. | Predict Secondary Structure, protein analysis, secondary structure prediction, protein sequence, sequence analysis, protein, analysis |
is listed by: Debian is listed by: SoftCite has parent organization: University College London; London; United Kingdom |
Biotechnology and Biological Science Research Council ; University College London |
DOI:10.1093/nar/gkz297 | Free, Freely available | SCR_018546, nlx_156884 | https://sources.debian.org/src/psipred/ | SCR_010246 | PSIPRED Protein Sequence Analysis Workbench, PSIPRED 4.0 | 2026-02-14 02:01:43 | 1688 |
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