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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://shimadzu.com.au/labsolutions

Software package for data analysis by Shimadzu Oceania.

Proper citation: LabSolutions (RRID:SCR_018241) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.vistrails.org/

Open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. It was designed to manage these rapidly-evolving workflows. VisTrails has a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the workflows that derive these products and their executions. This information is persisted as XML files or in a relational database, and it allows users to navigate workflow versions in an intuitive way, to undo changes but not lose any results, to visually compare different workflows and their results, and to examine the actions that led to a result. It also enables a series operations and user interfaces that simplify workflow design and use, including the ability to create and refine workflows by analogy and to query workflows by example. VisTrails supports the creation and execution of workflows. It allows the combination of loosely-coupled resources, specialized libraries, grid and Web services. The released version comes with support for several packages including, VTK, Image Magick, Web Services, and pylab. You can also download packages contributed by users, as well as create your own packages/modules. Workflows can be run interactively, through the VisTrails GUI, or in batch using a VisTrails server. VisTrails is written in Python and it uses the multi-platform Qt library for its user interface. It runs on Mac, Linux and Windows. Provenance-rich results derived by VisTrails can be included in LaTeX, Wiki, Microsoft Word and PowerPoint documents.

Proper citation: VisTrails (RRID:SCR_006261) Copy   

•   Source: SciCrunch Registry

http://www.tree-puzzle.de

Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.

Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy   

•   Source: SciCrunch Registry

http://www.cnprc.ucdavis.edu/research/arc.aspx

The Analytical and Resource Core provides services and resources to the scientific research community in areas including hematology, clinical chemistry, genetics, immunology, endocrinology, flow cytometry, and pathogen detection. Available resources include biological specimens, viral stocks, DNA, and species-specific reagents. Scientists and staff associated with each of the seven Core Laboratories provide consultation in experimental design, sample collection, and data analysis, and offer assays that utilize species-specific reagents wherever possible. Core Laboratory scientists can also work with users to develop new assays to meet research needs. Training is available for all assays, and Core Laboratories equipment can be made available, typically on a recharge basis. Nonhuman primate resources developed at CNPRC are available to qualified individuals via the Resource Services component of the Core. * Clinical Laboratory * Endocrine Core Laboratory * Flow Cytometry Core Laboratory * Genetics Core Laboratory * Infectious Diseases Immunology Core Laboratory * Pathogen Detection Core Laboratory * Respiratory Disease Immunology Core Laboratory * Affiliated Laboratory: Clinical Proteomics Core Laboratory * Affiliated Laboratory: Microarray Core Facility * Resource Services: The following research resources of CNPRC are available to scientists on a recharge basis. ** Allergen: Characterized protein extracts of house dust mite (Dermatophagoides pteronyssinus and Dermatophagoides farinae) are available for allergen sensitization projects. ** Biological Specimens: Tissues collected at necropsy are available from rhesus monkeys (Macaca mulatta), cynomolgus monkeys (Macaca fascicularis), and titi monkeys (Callicebus cupreus). Contact: Biospecimens (at) primate.ucdavis.edu Blood samples are available through our blood donor program. ** Data: Data for colony animals are available from our computerized database. Data include birth records, weights, reproductive history, relocation history, etc. ** DNA: DNA extracted from peripheral blood mononuclear cells is available on animals of all age-sex classes from known pedigrees. ** Reagents and Samples: Reagents, controls, and known/unknown samples are available from the Pathogen Detection Core Laboratory. Samples include pedigreed sera/plasma, fixed tissues and DNA from macaques and various other species. Validated reagents for many pathogens are available, including SIV, SRV1-5, SFV, STLV, RRV, RhCMV, Herpes B, SV40, and LCV. More information is available at: http://pdl.primate.ucdavis.edu/PDLreagents.html. ** Shipping: Shipping services are available by trained staff who can properly document, package and ship critical experimental materials, including nonhuman primate samples. Assistance is also provided for obtaining CITES permits, required for international shipment of any nonhuman primate samples. ** Transformed B-Cell Lines: Cryopreserved Herpes papio - transformed B cell lines from over 300 rhesus monkeys in the CNPRC colony are available. Transformation of macaque B cells to establish a new cell line is available on request. ** Virus Stock: Rhesus Cytomegalovirus: A unique primary isolate, developed at CNPRC, is available. ** Virus Stock: Simian Immunodeficiency Virus: Aliquots of SIVmac251 and SIVmac239 virus stocks were prepared by propagation in peripheral blood mononuclear cells from rhesus macaques and contain approximately 100,000 50% tissue culture infectious doses per ml. As measured by the commercial SIV branched chain assay, SIVmac251 contains 2 x 109 copies of SIV RNA per ml and SIVmac239 contains 109 copies of SIV RNA per ml. These virus stocks are infectious for rhesus macaques by intravenous, intravaginal and oral routes of inoculation.

Proper citation: California National Primate Research Center Analytical and Resource Core (RRID:SCR_000696) Copy   

•   Source: SciCrunch Registry

http://amide.sourceforge.net/index.html

Software tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+ and runs on any system that supports this toolkit (Linux, Windows, Mac OS X, etc.). The program incorporates automatic non-orthogonal data reslicing, allowing multiple data set to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library.

Proper citation: amide (RRID:SCR_005940) Copy   

•   Source: SciCrunch Registry

https://www.xsede.org/

XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools.

Proper citation: XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) Copy   

•   Source: SciCrunch Registry

https://github.com/jmchandonia/CORAL

Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis.

Proper citation: CORAL (RRID:SCR_022711) Copy   

•   Source: SciCrunch Registry

https://www.pinnaclet.com/sleepPRO.html

Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported.

Proper citation: Sirenia Sleep Pro (RRID:SCR_022918) Copy   

•   Source: SciCrunch Registry

http://sbi.postech.ac.kr/oasis/introduction/

A tool for various statistical tasks involved in analyzing survival data which provides a uniform platform to facilitate efficient statistical analyses of survival data in the aging field. The statistical features of OASIS include the calculation of Kaplan-Meier estimates, mean/median lifespan, mortality rate, Mantel-Cox Log-Rank test, Fishers exact test, weighted Log-Rank test, Kolmogorov-Smirnov test and Neymans smooth test. Moreover, OASIS generates survival and mortality curves that can be easily exported and modified by using common graphic softwares.

Proper citation: Online Application for Survival Analysis (OASIS) (RRID:SCR_014450) Copy   

•   Source: SciCrunch Registry

https://long-read-tools.org/

Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies.

Proper citation: long-read-tools (RRID:SCR_019116) Copy   

•   Source: SciCrunch Registry

https://openwetware.org/wiki/RAVE

Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG).

Proper citation: RAVE (RRID:SCR_019040) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/PAM-PIE/PAM

Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities.

Proper citation: PAM (RRID:SCR_020966) Copy   

•   Source: SciCrunch Registry

https://www.bmglabtech.com/mars-data-analysis-software/

Proprietary software package for data analysis by BMG Labtech.

Proper citation: MARS Data Analysis Software (RRID:SCR_021015) Copy   

•   Source: SciCrunch Registry

https://www.miltenyibiotec.com/products/macs-flow-cytometry/software/flowlogic-software.html

Software tool for flow cytometry data analysis by Miltenyi Biotec.

Proper citation: Flowlogic (RRID:SCR_020942) Copy   

•   Source: SciCrunch Registry

https://lung.hugeamp.org/

Portal enables browsing, searching, and analysis of human genetic information linked to lung diseases and related traits, while protecting integrity and confidentiality of underlying data.

Proper citation: Lung Disease Knowledge Portal (RRID:SCR_021352) Copy   

•   Source: SciCrunch Registry