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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | software application, web application, software resource, data analysis software, sequence analysis software, data processing software | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-02-11 10:57:48 | 3542 | |||||
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Research Randomizer Resource Report Resource Website 1000+ mentions |
Research Randomizer (RRID:SCR_008563) | data access protocol, software resource, web service | This site is designed for researchers and students who want a quick way to generate random numbers or assign participants to experimental conditions. Research Randomizer can be used in a wide variety of situations, including psychology experiments, medical trials, and survey research. The program uses a JavaScript random number generator to produce customized sets of random numbers. Since its release in 1997, Research Randomizer has been used to generate number sets over 10.7 million times. This service is part of Social Psychology Network and is fast, free, and runs with any recent web browser as long as JavaScript isn''t disabled. Research Randomizer is a free service offered to students and researchers interested in conducting random assignment and random sampling. By using this service, you agree to abide by the SPN User Policy and to hold Research Randomizer and its staff harmless in the event that you experience a problem with the program or its results. Although every effort has been made to develop a useful means of generating random numbers, Research Randomizer and its staff do not guarantee the quality or randomness of numbers generated. Any use to which these numbers are put remains the sole responsibility of the user who generated them. What are the system requirements needed to run Research Randomizer? This program works best with Firefox and other recent web browsers. If you''re using a browser that came with America Online, or older browsers made prior to 2003, you may experience some difficulties with Research Randomizer. You may also not be able to use Research Randomizer with some limited-function browsers that do not fully support JavaScript, such as the Opera broswer used on certain game consoles. We would suggest that you update to a fairly recent, fully- functional stand-alone browser. How do I know what browser I am using? The easiest way to find this out is to click Help on the pulldown menu at the top of the screen. One of the options should be About Mozilla Firefox, About Internet Explorer, About Netscape, or something similar. Selecting this option will open a window that displays the name, version number, and copyright date of your browser. How does Research Randomizer generate its numbers? Research Randomizer uses the Math.random method within the JavaScript programming language to generate its random numbers for all modern web browsers. If you are using an older version of Microsoft Internet Explorer or Netscape Navigator (that is prior to version 4.0 of either), Research Randomizer uses an adaptation of the Central Randomizer by Paul Houle. Note that Research Randomizer no longer supports much-older browsers by other vendors (e.g., Mosaic). Who designed Research Randomizer? The original idea and programming for Research Randomizer came from Geoffrey C. Urbaniak in 1997. Research Randomizer was then jointly developed with Scott Plous, webmaster of Social Psychology Network, and online tutorials were added to the main program. In 1999 the site was redesigned with the assistance of Mike Lestik, in 2003 Mike Lestik added the download function, and in 2007 Mike Lestik and Scott Plous redesigned the site and added new content. | is listed by: SoftCite | nif-0000-31448 | SCR_008563 | Research Randomizer | 2026-02-11 10:58:00 | 2093 | ||||||||||
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MODELLER Resource Report Resource Website 5000+ mentions |
MODELLER (RRID:SCR_008395) | portal, software application, data or information resource, simulation software, software resource, topical portal | Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms. | comparative, protein, structure, modelling, satisfaction, spatial, restrain, homology, 3D, alignment, sequence, hydrogen, atom, cluster |
is listed by: SoftCite has parent organization: University of California at San Francisco; California; USA |
Sandler Family Supporting Foundation ; NIGMS R01 GM54762; NIGMS P01 GM71790; NIH P01 A135707; NIGMS U54 GM62529; IBM ; Intel |
Restricted | nif-0000-30054 | SCR_008395 | 2026-02-11 10:57:50 | 5736 | ||||||||
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MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | software resource, software application, data processing software, data analysis software | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach https://bio.tools/mach |
https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-02-11 10:57:58 | 925 | |||||
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STAR Resource Report Resource Website 10000+ mentions |
STAR (RRID:SCR_004463) | alignment software, software application, image analysis software, software resource, data processing software | Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. | RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools |
is used by: STARsolo is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U54 HG004557 | PMID:23104886 DOI:10.1093/bioinformatics/bts635 |
biotools:star, OMICS_01254, SCR_015899 | https://github.com/alexdobin/STAR https://bio.tools/star https://sources.debian.org/src/rna-star/ |
SCR_004463 | Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner | 2026-02-11 10:56:54 | 22809 | ||||||
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MycoBank Resource Report Resource Website 500+ mentions |
MycoBank (RRID:SCR_004950) | MycoBank | data repository, data or information resource, database, service resource, storage service resource | Database documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated and will also serve as Life Science Identifiers (LSIDs). Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural errors; however, no censorship whatsoever, (nomenclatural or taxonomic) will be exerted by MycoBank. Deposited names will remain -when desired- strictly confidential until after publication, and will then be accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases to realize a species bank that eventually will link all databases of life. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative. For the moment 2 search engines are available from the MycoBank website. The first one permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. The second is dedicated to bibliographic queries related to fungal name''''s publications. MycoBank users willing to deposit their data will have to register so that they willbe able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and to avoid fake entries. | yeast, aspergillus, penicillium, phaeoacremonium, russula, resupinate russulales, mycosphaerella, trichomycete, arthropod, hysteriaceae, mytilinidiaceae, mycology, nomenclature, life science identifier, bibliography, sequence alignment, polyphasic identification, image collection, FASEB list |
is listed by: SoftCite is related to: Index Fungorum |
PMID:24563843 | nlx_91803, r3d100011222 | https://doi.org/10.17616/R39D0Q | SCR_004950 | 2026-02-11 10:57:07 | 743 | |||||||
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TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | software application, alignment software, image analysis software, software resource, data analysis software, sequence analysis software, data processing software | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat https://bio.tools/tophat https://sources.debian.org/src/tophat/ |
http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-02-11 10:58:40 | 9575 | ||||
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minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | software application, data visualization software, software resource, data analysis software, data processing software | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi https://bio.tools/minfi https://bio.tools/minfi |
SCR_012830 | 2026-02-11 10:58:39 | 390 | ||||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | software resource, software application, data processing software, data analysis software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy https://sources.debian.org/src/r-bioc-affy/ |
SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-02-11 10:58:45 | 2996 | ||||
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WebPlotDigitizer Resource Report Resource Website 1000+ mentions |
WebPlotDigitizer (RRID:SCR_013996) | data access protocol, service resource, software resource, web service | Web based tool to extract data from plots, images, and maps. HTML5 based online tool to extract numerical data from plot images. Used to reverse engineer images of data visualizations to extract underlying numerical data. | Data extraction, plot, image, map, HTML5, numerical data extraction, plot image, reverse image, reverse data visualization |
is listed by: SoftCite is related to: Connected Researchers |
Free, Available for download, Freely available | https://apps.automeris.io/wpd/ https://github.com/ankitrohatgi/WebPlotDigitizer https://github.com/ankitrohatgi/WebPlotDigitizer/releases |
http://arohatgi.info/WebPlotDigitizer/ | SCR_013996 | WebPlotDigitizer Version 4.1, WebPlotDigitizer Version 4.2 | 2026-02-11 10:58:58 | 1786 | |||||||
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Phaser Resource Report Resource Website 1000+ mentions |
Phaser (RRID:SCR_014219) | image reconstruction software, software application, image analysis software, software resource, data processing software, data acquisition software | Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods. | crystallographic software, molecular replacement, experimental phasing method, data acquisition software, image analysis software, image reconstruction software |
is listed by: SoftCite is affiliated with: Phenix has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:19461840 | Available through Phenix, Available through CCP4, Acknowledgement requested | http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software | SCR_014219 | 2026-02-11 10:58:53 | 2572 | ||||||||
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Coot Resource Report Resource Website 10000+ mentions |
Coot (RRID:SCR_014222) | COOT | software application, model, data or information resource, simulation software, software resource, software toolkit | Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available. | software toolkit, simulation software, model manipulation, protein modeling, bio.tools |
is used by: PDB-REDO is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MolProbity has parent organization: MRC Laboratory of Molecular Biology |
PMID:15572765 | Available for download, Acknowledgement requested | biotools:coot | http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot https://bio.tools/coot |
SCR_014222 | Crystallographic Object-Oriented Toolkit | 2026-02-11 10:59:02 | 14789 | |||||
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Nanoparticle Tracking Analysis Resource Report Resource Website 10+ mentions |
Nanoparticle Tracking Analysis (RRID:SCR_014239) | NTA | data acquisition software, software application, software resource, data processing software | Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation. | data acquisition software, particle size distribution, liquid suspension | is listed by: SoftCite | Pay for product | SCR_014239 | Nanoparticle Tracking Analysis (NTA) | 2026-02-11 10:58:53 | 28 | ||||||||
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JMP Resource Report Resource Website 100+ mentions |
JMP (RRID:SCR_014242) | software application, data visualization software, data management software, software resource, data processing software | Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design. | statistical software, data visualization, data management, graphic data visualization |
is listed by: Metabolomics Workbench is listed by: SoftCite |
Pay for product, Free trial download is available | SCR_014242 | 2026-02-11 10:58:53 | 190 | ||||||||||
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NIS-Elements Resource Report Resource Website 1000+ mentions Rating or validation data |
NIS-Elements (RRID:SCR_014329) | software application, software resource, software toolkit, data analysis software, data processing software | Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | element, microscope imaging software, software suite, nikon |
is listed by: SoftCite works with: Nikon ECLIPSE Ti2 inverted microscope |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014329 | Nikon Instruments Software Elements, NIS Elements, Nikon Instruments Software | 2026-02-11 10:58:54 | 3462 | |||||||||
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IMAGIC Resource Report Resource Website 100+ mentions |
IMAGIC (RRID:SCR_014447) | software application, image analysis software, software resource, data processing software, image processing software | An image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules. | image analysis, spectra, multi-dimensional data, macromolecule, 3d processing, tomograph, spectrometer, software environment | is listed by: SoftCite | PMID:8742718 | Commercial, Account needed for download | SCR_014447 | 2026-02-11 10:58:55 | 217 | |||||||||
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LSM Image Examiner Resource Report Resource Website 1000+ mentions Rating or validation data |
LSM Image Examiner (RRID:SCR_014344) | data management software, software application, software resource | Software used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area. | data management software, image archive, image management, interactive measurement | is listed by: SoftCite | Available for download | http://www.zeiss.com/microscopy/en_us/website/downloads/lsm-image-browser.html http://lsm-image-examiner.software.informer.com | SCR_014344 | LSM Image Browser | 2026-02-11 10:58:54 | 1508 | ||||||||
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MassLynx Resource Report Resource Website 5000+ mentions |
MassLynx (RRID:SCR_014271) | software application, data management software, software resource, data analysis software, data processing software, data acquisition software | Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data acquisition software, data analysis software, data management software, mass spectrometry | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014271 | MassLynx MS Software | 2026-02-11 10:58:53 | 5802 | |||||||||
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I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | software resource, software application, data processing software, data analysis software | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-02-11 10:58:59 | 3702 | |||||
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Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | software application, software resource, data analysis software, sequence analysis software, data processing software | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks https://bio.tools/cufflinks https://sources.debian.org/src/cufflinks/ |
SCR_014597 | 2026-02-11 10:58:58 | 8838 |
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