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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GeneMapper Resource Report Resource Website 5000+ mentions |
GeneMapper (RRID:SCR_014290) | sequence analysis software, software application, data processing software, data analysis software, software resource | Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment. | genotyping software, sequence analysis software, multiplication functionality, dna sizing, allele call, electrophoresis genotyping system | is listed by: SoftCite | Restricted | https://www.thermofisher.com/order/catalog/product/de/en/4370784, https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2F4476603A.pdf, | https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600798&tab=DetailInfo | SCR_014290 | , GeneMapper Software 5, GeneMapper Software 6, GeneMapper Software | 2026-08-03 09:35:35 | 5231 | |||||||
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NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | software application, data processing software, data analysis software, simulation software, software resource | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-08-03 09:36:29 | 42 | ||||||||
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SignalP Resource Report Resource Website 5000+ mentions |
SignalP (RRID:SCR_015644) | software resource, web application | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-08-03 09:36:12 | 9406 | |||||||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | software resource, data visualization software, software application, data processing software | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-08-03 09:31:56 | 2194 | |||||
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QuantPrime Resource Report Resource Website 100+ mentions |
QuantPrime (RRID:SCR_015498) | software resource, web application | Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes. | primer design, primer pair design, rt-qpcr, reverse transcription qpcr | is listed by: SoftCite | DOI:10.1186/1471-2105-9-465 | Acknowledgement requested, Available as a web application, Available as a desktop application | SCR_015498 | 2026-08-03 09:35:59 | 155 | |||||||||
|
ModFit LT Resource Report Resource Website 100+ mentions |
ModFit LT (RRID:SCR_016106) | software resource, data visualization software, software application, data processing software | Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software. | flow, cytometry, histogram, model, graph, cell, tracking, dye, cell line | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_016106 | Verity Software House ModFit LT | 2026-08-03 09:36:17 | 143 | |||||||||
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GRADEpro Resource Report Resource Website 100+ mentions |
GRADEpro (RRID:SCR_021308) | data management software, software resource, software application | Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables. | Summary of findings tables, cochrane systematic reviews, research evidence creating, research evidence management, research evidence sharing summaries, evidence profiles, | is listed by: SoftCite | Restricted | https://cebgrade.mcmaster.ca/gradepro.html | SCR_021308 | Guideline Development Tool, GRADEpro GDT, GDT, GRADE Guideline Development Tool, G2DT | 2026-08-03 09:37:19 | 376 | ||||||||
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software resource, data processing software, software application, data analysis software | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-08-03 09:36:57 | 25 | ||||||||
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PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | narrative resource, data or information resource, portal, standard specification | Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. | MDAR, standard, report standard, reporting reviews, randomized trial, evaluating randomized trial, reporting systematic review, intervention evaluation, meta analysis | is listed by: SoftCite | Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018721 | Preferred Reporting Items for Systematic Reviews and Meta-Analyses | 2026-08-03 09:37:19 | 1069 | |||||||
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Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | software resource, data processing software, software application, data analysis software | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-08-03 09:37:17 | 42 | ||||||
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ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | production service resource, software application, data processing software, analysis service resource, data analysis software, service resource, software resource | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | Extreme Limiting Dilution Analysis | 2026-08-03 09:37:21 | 385 | ||||||||
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igraph Resource Report Resource Website 100+ mentions |
igraph (RRID:SCR_019225) | network analysis software, network graph visualization software, software toolkit, software application, data processing software, data analysis software, software resource, data visualization software | Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus. | Graphs analysis, network analysis, generating graph function, graph visualization |
is listed by: CRAN is listed by: SoftCite is related to: igraph for R |
Free, Available for download, Freely available | https://igraph.org/, https://github.com/igraph/igraph/releases/tag/0.8.4 | SCR_019225 | igraph 0.8.4, igraph 1.2.6 | 2026-08-03 09:37:13 | 354 | ||||||||
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OpenClinica Resource Report Resource Website 10+ mentions |
OpenClinica (RRID:SCR_019223) | data acquisition software, software resource, software application, data processing software | Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system. | Clinical trial, data management system, clinical trial management system, clinical data, clinical data management | is listed by: SoftCite | PMID:21893916 | Restricted | https://www.openclinica.com/community-edition-open-source-edc/ | SCR_019223 | 2026-08-03 09:37:12 | 35 | ||||||||
|
PROCHECK Resource Report Resource Website 50+ mentions |
PROCHECK (RRID:SCR_019043) | software resource, data processing software, software application, data analysis software | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-08-03 09:37:08 | 75 | |||||||||
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CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | software resource, data processing software, software application, data analysis software | Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | CalcuSyn Version 2.0 | 2026-08-03 09:37:29 | 57 | |||||||||
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Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | software resource, data processing software, software application, data analysis software | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-08-03 09:37:14 | 74 | |||||||||
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MutationAssessor Resource Report Resource Website 500+ mentions |
MutationAssessor (RRID:SCR_005762) | mutationassessor.org | data analysis service, service resource, analysis service resource, production service resource | A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cancer, protein, mutation, function, amino-acid, substitution |
is listed by: OMICtools is listed by: SoftCite |
PMID:21727090 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00134, nlx_149228 | SCR_005762 | MutationAssessor - functional impact of protein mutations, MutationAssessor - functional impact of mutations, mutationassessor.org - functional impact of protein mutations | 2026-08-03 09:32:47 | 669 | ||||||
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mitopred Resource Report Resource Website 1+ mentions |
mitopred (RRID:SCR_006135) | MITOPRED | data analysis service, service resource, analysis service resource, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution. | yeast, c. elegans, drosophila, mouse, human, arabidopsis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University at Albany; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mitopred, nif-0000-03956, BioTools:mitopred | https://bio.tools/mitopred, https://bio.tools/mitopred, https://bio.tools/mitopred | SCR_006135 | A genome-scale method for predicting mitochondrial proteins | 2026-08-03 09:32:54 | 7 | ||||||
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GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | Generic Genome Browser | 2026-08-03 09:33:11 | 43 | ||||
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Primer-BLAST Resource Report Resource Website 5000+ mentions |
Primer-BLAST (RRID:SCR_003095) | Primer-BLAST | data analysis service, service resource, analysis service resource, production service resource | A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications. | primer, blast, pcr target, polymerase chain reaction, primer design |
is listed by: OMICtools is listed by: SoftCite is related to: Primer3 has parent organization: NCBI |
PMID:22708584 | Free, Freely available | OMICS_02343 | SCR_003095 | 2026-08-03 09:31:57 | 5498 |
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