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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://sciex.com/products/software/analyst-tf-software
Acquisition software for mass spectrometry data from TripleTOF instrument(s). Analyst provides functionality for instrument control, data analysis, reporting, and audit trail.
Proper citation: Analyst®TF Software (RRID:SCR_015785) Copy
http://mtshasta.phys.washington.edu/website/SuperSegger.php
Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells.
Proper citation: SuperSegger (RRID:SCR_018532) Copy
https://github.com/theislab/scanpy
Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.
Proper citation: scanpy (RRID:SCR_018139) Copy
https://gitlab.com/alexmascension/triku
Software tool as feature selection method based on nearest neighbors for single-cell data.
Proper citation: triku (RRID:SCR_020977) Copy
https://shimadzu.com.au/labsolutions
Software package for data analysis by Shimadzu Oceania.
Proper citation: LabSolutions (RRID:SCR_018241) Copy
http://www.functionalglycomics.org/static/consortium/consortium.shtml
The Consortium for Functional Glycomics (CFG) serves to combine the expertise and glycomics resources to reveal functions of glycans and glycan-binding proteins (GBPs) that impact human health and disease. The CFG offers resources to the community free of charge, including glycan array screening services, a reagent bank, and access to a large glycomics database and data analysis tools.
Proper citation: Consortium for Functional Glycomics (CFG) (RRID:SCR_013689) Copy
https://en.freedownloadmanager.org/Windows-PC/Flowing-Software-FREE.html
Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc.
Proper citation: Flowing Software 2.5.1 (RRID:SCR_015781) Copy
https://github.com/kscottz/SkinnerBox
Software tool for data logging and analysis.
Proper citation: Skinner Box (RRID:SCR_021514) Copy
https://www.ibm.com/products/spss-statistics
Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY.
Proper citation: IBM SPSS Statistics (RRID:SCR_016479) Copy
http://ntap.cbi.pku.edu.cn/usage.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl.
Proper citation: NTAP (RRID:SCR_001488) Copy
Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP.
Proper citation: CLIP-Explorer (RRID:SCR_018128) Copy
A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available.
Proper citation: StatCrunch (RRID:SCR_013992) Copy
A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as "bundles" with other users, who can edit and download them.
Proper citation: Wakari (RRID:SCR_013995) Copy
http://www.nitrc.org/projects/aperture/
A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures.
Proper citation: APERTURE (RRID:SCR_014082) 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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