Tools   Select Another Resource Report Type

https://github.com/sapporo-wes/yevis-cli

Software CLI tool to support building and maintaining Yevis workflow registry.

Proper citation: Yevis cli (RRID:SCR_023204) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=Rtrack

Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.

Proper citation: Rtrack (RRID:SCR_023025) Copy   

•   Source: SciCrunch Registry

https://www.dtu.ox.ac.uk/homacalculator/

Software tool used to calculate Homeostasis Model Assessment which takes account of variations in hepatic and peripheral glucose resistance, increases in insulin secretion curve for plasma glucose concentrations and contribution of circulating proinsulin. Provides access to HOMA2 model for researchers who wish to use model derived estimates of %B and %S, rather than linear approximations.

Proper citation: HOMA2 calculator (RRID:SCR_023419) Copy   

•   Source: SciCrunch Registry

https://www.vitalimages.com/enterprise-imaging-solution/diagnostic-viewer/

Software application providing tools and features that may be used for general purpose radiological viewing and reading of image data from various imaging modalities, clinical review and performs functions of digital image processing, measurement, communications and storage.

Proper citation: Vitrea Read Diagnostic Viewer (RRID:SCR_023418) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/merqury

Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers.

Proper citation: Merqury (RRID:SCR_022964) Copy   

•   Source: SciCrunch Registry

https://github.com/Kinggerm/GetOrganelle

Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes.

Proper citation: GetOrganelle (RRID:SCR_022963) Copy   

•   Source: SciCrunch Registry

https://github.com/CJ-Chen/TBtools-Manual

Software integrative toolkit developed for interactive analyses of big biological data.

Proper citation: TBtools (RRID:SCR_023018) Copy   

•   Source: SciCrunch Registry

https://github.com/JustinChu/JupiterPlot

Software pipeline for generating Circos based genome assembly consistency plot given set of contigs relative to reference genome. Intended to visualize large scale translocations or missassemblies in draft assemblies, but it can also be useful when trying to show synteny between whole genomes.Circos based tool to visualize genome assembly consistency

Proper citation: JupiterPlot (RRID:SCR_022961) Copy   

•   Source: SciCrunch Registry

https://github.com/virajbdeshpande/AmpliconArchitect

Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers.

Proper citation: AmpliconArchitect (RRID:SCR_023150) Copy   

•   Source: SciCrunch Registry

https://www.beckman.com/liquid-handlers/software/sami-ex#product-table-wrapper

Software tool provides automation and process control across wide variety of applications, creates planned data driven schedules in optimized and predictable scheduling environment.

Proper citation: SAMI Ex (RRID:SCR_023271) Copy   

•   Source: SciCrunch Registry

https://github.com/findCP/findCPcli

Software command line Python package for computation of chokepoint reactions in genome scale metabolic models. Used to compute chokepoints by taking into account both topology and dynamic information of network. Can compute and remove dead-end metabolites, find essential reactions and update flux bounds of reactions according to results of Flux Variability Analysis.

Proper citation: findCPcli (RRID:SCR_023391) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/mitochondria-simulator

Software repository for mtDNA assembly project.

Proper citation: mitochondria simulator (RRID:SCR_023430) Copy   

•   Source: SciCrunch Registry

https://trabucayre.github.io/openFPGALoader

Universal utility for programming FPGAs. Compatible with many boards, cables and FPGA from major manufacturers (Xilinx, Altera/Intel, Lattice, Gowin, Efinix, Anlogic, Cologne Chip). Works on Linux, Windows and macOS.

Proper citation: openFPGALoader (RRID:SCR_023153) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/synchCams/

Software toolbox for synchronized dual camera acquisition. Library for acquisition of synchronized dual camera video. Videos are saved with alternate acquisition of frames what ensures equal number of frames.

Proper citation: synchCams (RRID:SCR_023152) Copy   

•   Source: SciCrunch Registry

https://www.beckman.com/liquid-handlers/software/dart

Software package that gathers data and synthesizes runtime information from Biomek log files to capture each manipulation of sample during course of method.

Proper citation: Data Acquisition and Reporting Tool (RRID:SCR_023272) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=sf

Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization.

Proper citation: Simple Features (RRID:SCR_023393) Copy   

•   Source: SciCrunch Registry

http://szhorvat.net/pelican/igraphm-a-mathematica-interface-for-igraph.html

Software package for use in complex networks and graph theory research. Mathematica interface for igraph. Provides Mathematica interface to popular igraph network analysis package, as well as many other functions for working with graphs in Mathematica. IGraph/M comes pre-packaged and ready to use on Windows, OS X and Linux (64-bit Intel), as well as the Raspberry Pi computer. The code is open source and can be compiled on other platforms as well (such as 32-bit Windows).

Proper citation: iGraph/M (RRID:SCR_023308) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/repfinder

Software tool to find shared repeats between mitochondrial genomes.

Proper citation: RepFinder (RRID:SCR_023429) Copy   

•   Source: SciCrunch Registry

https://github.com/qianli10000/mtradeR

Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.

Proper citation: mtradeR (RRID:SCR_022977) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/omicsGAN

Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.

Proper citation: OmicsGAN (RRID:SCR_022976) Copy   

•   Source: SciCrunch Registry