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https://github.com/blackrim/phyutility
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.
Proper citation: Phyutility (RRID:SCR_018545) Copy
Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops.
Proper citation: CuGenDB (RRID:SCR_018401) Copy
https://imspectordocs.readthedocs.io/en/latest/intro.html
Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results.
Proper citation: Imspector (RRID:SCR_018863) Copy
https://github.com/biocatiit/musclex
Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data.
Proper citation: Muscle X (RRID:SCR_018811) Copy
Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables.
Proper citation: UCSC Xena (RRID:SCR_018938) Copy
Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response.
Proper citation: o²S²PARC (RRID:SCR_018997) Copy
https://nanopore.usegalaxy.eu/
Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.
Proper citation: NanoGalaxy (RRID:SCR_018912) Copy
http://www.nonlinear.com/progenesis/qi-for-proteomics/
Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.
Proper citation: Progenesis QI (RRID:SCR_018923) Copy
https://github.com/davidebolo1993/TRiCoLOR
Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.
Proper citation: TRiCoLOR (RRID:SCR_018801) Copy
http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/
Software Matlab toolbox to perform representational similarity analysis for neural data.
Proper citation: Toolbox for Representational Similarity Analysis (RRID:SCR_019029) Copy
Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories.
Proper citation: IDseq (RRID:SCR_019038) Copy
https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation
Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer.
Proper citation: CLIP Tool Kit (RRID:SCR_019034) Copy
Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource.
Proper citation: NEMAR (RRID:SCR_019100) Copy
https://CRAN.R-project.org/package=tidyverse
Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.
Proper citation: tidyverse (RRID:SCR_019186) Copy
http://www.nitrc.org/projects/niistat/
A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data.
Proper citation: NiiStat (RRID:SCR_014152) Copy
Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization.
Proper citation: COPASI (RRID:SCR_014260) Copy
http://www.starrlifesciences.com/products/vitalview-software
A data acquisition and analysis software program. The program collects data from sensors and receivers and displays graphical data analysis as well as descriptive statistics.
Proper citation: VitalView Software (RRID:SCR_014497) Copy
http://cyberinncorp.com/SigmaGel.htm
Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images.
Proper citation: SigmaGel Software (RRID:SCR_014598) Copy
http://statplus-mac.en.softonic.com/mac
A statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program.
Proper citation: StatPlus Mac (RRID:SCR_014635) Copy
http://www6.appliedbiosystems.com/support/software/copycaller/CopyCallerUserGuide.pdf
A software for analyzing real-time PCR data and quantifying DNA targets. It can perform copy number analysis, report confidence in copy number, display data in table and graphic format, change analysis parameters, and view data analysis information for multiple experiments at once.
Proper citation: CopyCaller (RRID:SCR_014486) Copy
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