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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | SciCrunch Registry | 2026-10-17 01:28:49 | 72 | ||||||||
|
TreeView Resource Report Resource Website 1000+ mentions |
TreeView (RRID:SCR_013503) | TreeView | software resource | Software to graphically browse results of clustering and other analyses from Cluster. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1093/bioinformatics/bth349 | OMICS_01574 | https://sources.debian.org/src/treeview/ | SCR_013503 | SciCrunch Registry | 2026-10-17 01:28:43 | 2754 | ||||||||
|
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 | SciCrunch Registry | WebPlotDigitizer Version 4.1, WebPlotDigitizer Version 4.2 | 2026-10-17 01:28:48 | 2274 | |||||||
|
Nanoparticle Tracking Analysis Resource Report Resource Website 10+ mentions |
Nanoparticle Tracking Analysis (RRID:SCR_014239) | NTA | data acquisition software, data processing software, software application, software resource | 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 | SciCrunch Registry | Nanoparticle Tracking Analysis (NTA) | 2026-10-17 01:28:44 | 29 | ||||||||
|
JMP Resource Report Resource Website 100+ mentions |
JMP (RRID:SCR_014242) | data management software, data processing software, data visualization software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:28:38 | 207 | ||||||||||
|
Phaser Resource Report Resource Website 1000+ mentions |
Phaser (RRID:SCR_014219) | data acquisition software, data processing software, image analysis software, image reconstruction software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:28:59 | 2664 | ||||||||
|
Coot Resource Report Resource Website 10000+ mentions |
Coot (RRID:SCR_014222) | COOT | data or information resource, model, simulation software, software application, 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 | SciCrunch Registry | Crystallographic Object-Oriented Toolkit | 2026-10-17 01:28:38 | 15682 | |||||
|
MolProbity Resource Report Resource Website 5000+ mentions |
MolProbity (RRID:SCR_014226) | software resource, web application | A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot. | web application, consultation, macromolecular structure, structure validation, macromolecular crystallography |
is listed by: SoftCite is related to: Phenix is related to: Coot has parent organization: Duke University; North Carolina; USA |
Howard Hughes Medical Institute Predoctoral Fellowship ; NIGMS GM-15000; NIGMS GM-61302 |
DOI:10.1107/S0907444909042073 | Acknowledgement requested, Requires Java and Javascript | https://www.phenix-online.org/documentation/reference/molprobity_tool.html | SCR_014226 | SciCrunch Registry | 2026-10-17 01:28:38 | 6711 | |||||||
|
MassLynx Resource Report Resource Website 5000+ mentions |
MassLynx (RRID:SCR_014271) | data acquisition software, data analysis software, data management software, data processing software, software application, software resource | 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 | SciCrunch Registry | MassLynx MS Software | 2026-10-17 01:28:39 | 5809 | |||||||||
|
Minitab Resource Report Resource Website 5000+ mentions |
Minitab (RRID:SCR_014483) | data analysis software, data processing software, software application, software resource | A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment. | data analysis, statistical analysis, hypothesis, confidence, descriptive | is listed by: SoftCite | SCR_014483 | SciCrunch Registry | 2026-10-17 01:28:47 | 6109 | |||||||||||
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NIS-Elements Resource Report Resource Website 1000+ mentions Rating or validation data |
NIS-Elements (RRID:SCR_014329) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | Nikon Instruments Software Elements, NIS Elements, Nikon Instruments Software | 2026-10-17 01:28:45 | 3515 | |||||||||
|
IMAGIC Resource Report Resource Website 100+ mentions |
IMAGIC (RRID:SCR_014447) | data processing software, image analysis software, image processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:28:42 | 217 | |||||||||
|
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 | SciCrunch Registry | LSM Image Browser | 2026-10-17 01:28:40 | 1520 | ||||||||
|
Definiens Developer XD Resource Report Resource Website 10+ mentions |
Definiens Developer XD (RRID:SCR_014283) | software resource | A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation. | development environment, image analysis solution, segmentation, classification, image analysis algorithm library, tissue microarray, whole slide image, tissue studio | is listed by: SoftCite | SCR_014283 | SciCrunch Registry | 2026-10-17 01:28:50 | 11 | |||||||||||
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I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-10-17 01:29:04 | 3874 | |||||
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Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:29:04 | 9083 | |||||||
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COMSOL Multiphysics Resource Report Resource Website 50+ mentions |
COMSOL Multiphysics (RRID:SCR_014767) | simulation software, software application, software resource | General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating. | simulation software, software platform, physics, problem solver | is listed by: SoftCite | Commercially available | SCR_014767 | SciCrunch Registry | 2026-10-17 01:29:06 | 51 | ||||||||||
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CVODE Resource Report Resource Website 50+ mentions |
CVODE (RRID:SCR_014696) | data analysis software, data processing software, software application, software resource | Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, solver, equation solver, ordinary differential equation, differential equation, stiff, nonstiff | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014696 | SciCrunch Registry | SUNDIALS CVODE | 2026-10-17 01:28:55 | 56 | |||||||||
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MedCalc Resource Report Resource Website 10000+ mentions |
MedCalc (RRID:SCR_015044) | data analysis software, data processing software, software application, software resource | Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis. | statistic, statistical analysis, roc curve, reference software | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_015044 | SciCrunch Registry | 2026-10-17 01:28:58 | 19712 | ||||||||||
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KaleidaGraph Resource Report Resource Website 1000+ mentions |
KaleidaGraph (RRID:SCR_014980) | data analysis software, data processing software, data visualization software, software application, software resource | Data analysis, graphing, and management application that allows users to import, manipulate, analyze data, and create customized plots. Plots include x-y probability, histogram, box, percentile, horizontal bar, stack bar, column, stack column, polar, and pie. Binned data can be exported to a histogram, step plot, or spike plot. KaleidaGraph works with Windows and Macintosh systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | custom graph, custom plot, publishable graph, publishable plot, data manipulation, curve fitting | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014980 | SciCrunch Registry | 2026-10-17 01:29:08 | 2789 |
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