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http://bioconductor.org/packages/release/bioc/html/topGO.html

Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Proper citation: topGO (RRID:SCR_014798) Copy   

•   Source: SciCrunch Registry

http://www.hologic.com

Commercial organization that provides services and products in global healthcare and diagnostics.

Proper citation: Hologic (RRID:SCR_015529) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/eeglab/

Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. First developed on Matlab 5.3 under Linux, EEGLAB runs on Matlab v5 and higher under Linux, Unix, Windows, and Mac OS X (Matlab 7+ recommended). EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users'' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB ''datasets'' and/or across a collection of datasets brought together in an EEGLAB ''studyset.'' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data. For creative research programmers and methods developers, EEGLAB offers an extensible, open-source platform through which they can share new methods with the world research community by publishing EEGLAB ''plug-in'' functions that appear automatically in the EEGLAB menu of users who download them. For example, novel EEGLAB plug-ins might be built and released to ''pick peaks'' in ERP or time/frequency results, or to perform specialized import/export, data visualization, or inverse source modeling of EEG, MEG, and/or ECOG data. EEGLAB Features * Graphic user interface * Multiformat data importing * High-density data scrolling * Defined EEG data structure * Open source plug-in facility * Interactive plotting functions * Semi-automated artifact removal * ICA & time/frequency transforms * Many advanced plug-in toolboxes * Event & channel location handling * Forward/inverse head/source modeling

Proper citation: EEGLAB (RRID:SCR_007292) 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

http://www.usadellab.org/cms/index.php?page=trimmomatic

Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

Proper citation: Trimmomatic (RRID:SCR_011848) 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

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.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

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.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