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https://www.webofscience.com/wos/woscc/advanced-search

Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database.

Proper citation: Web of Science (RRID:SCR_022706) Copy   

•   Source: SciCrunch Registry

http://www.gelifesciences.com/webapp/wcs/stores/servlet/catalog/en/GELifeSciences-us/products/AlternativeProductStructure_16016/29000605

Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImageQuant (RRID:SCR_014246) Copy   

•   Source: SciCrunch Registry

https://pathcore.bsd.uchicago.edu/Downloads/HTRC_ImageScUG.pdf

Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImageScope (RRID:SCR_014311) Copy   

•   Source: SciCrunch Registry

https://www.embl-hamburg.de/biosaxs/software.html

Software toolkit for small-angle scattering data analysis from biological macromolecules.

Proper citation: ATSAS (RRID:SCR_015648) Copy   

•   Source: SciCrunch Registry

http://www.waters.com/waters/en_PL/ProteinLynx-Global-SERVER-%28PLGS%29/nav.htm?cid=513821&locale=en_PL

Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems.

Proper citation: ProteinLynx Global Server (RRID:SCR_016664) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/maestro

Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.

Proper citation: Maestro (RRID:SCR_016748) Copy   

•   Source: SciCrunch Registry

http://www.cb.uu.se/~amin/BlobFinder/

Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell.

Proper citation: BlobFinder (RRID:SCR_015788) Copy   

•   Source: SciCrunch Registry

https://www.phenix-online.org/documentation/reference/refinement.html

Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB.

Proper citation: Phenix.refine (RRID:SCR_016736) Copy   

•   Source: SciCrunch Registry

https://www.indicalab.com/halo/

Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology.

Proper citation: HALO (RRID:SCR_018350) Copy   

•   Source: SciCrunch Registry

http://www.scipy.org/

A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.

Proper citation: SciPy (RRID:SCR_008058) Copy   

•   Source: SciCrunch Registry

http://www.sas.com

Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.

Proper citation: Statistical Analysis System (RRID:SCR_008567) Copy   

•   Source: SciCrunch Registry

http://www-genepi.med.utah.edu/Genie/

Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GENIE (RRID:SCR_009197) Copy   

•   Source: SciCrunch Registry

http://www.rna-society.org/rnalocate/

Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation.

Proper citation: RNALocate (RRID:SCR_024418) Copy   

•   Source: SciCrunch Registry

http://www.cuilab.cn/sramp/

Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.

Proper citation: SRAMP (RRID:SCR_024500) Copy   

•   Source: SciCrunch Registry

http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAfold.cgi

Web server predict secondary structures of single stranded RNA or DNA sequences.

Proper citation: RNAfold (RRID:SCR_024427) Copy   

•   Source: SciCrunch Registry

https://nano-measurer.software.informer.com/

Software tool to process micrograph images for particle size.

Proper citation: Nano Measurer (RRID:SCR_024493) Copy   

•   Source: SciCrunch Registry

https://topospro.com/software/

Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters.

Proper citation: ToposPro (RRID:SCR_024496) Copy   

•   Source: SciCrunch Registry

https://www.cs.cmu.edu/~jernst/stem/

Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology.

Proper citation: Stem (RRID:SCR_024499) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/product/cell-analysis/real-time-cell-metabolic-analysis/xf-software/seahorse-wave-controller-software-2-6-1-740904

Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis.

Proper citation: Agilent Seahorse Wave (RRID:SCR_024491) Copy   

•   Source: SciCrunch Registry

https://swissmodel.expasy.org/lddt

Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility.

Proper citation: lDDT (RRID:SCR_024524) Copy   

•   Source: SciCrunch Registry