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

Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately.

Proper citation: shinyhelper (RRID:SCR_022755) Copy   

•   Source: SciCrunch Registry
  

https://github.com/fritzsedlazeck/SURVIVOR

Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering.

Proper citation: SURVIVOR (RRID:SCR_022995) Copy   

•   Source: SciCrunch Registry
  

https://bids-matlab.readthedocs.io/en/latest/

Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format.

Proper citation: BIDS-Matlab (RRID:SCR_022292) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ZhiGroup/IBD_benchmark

Software package as open source project benchmarks IBD detection tools with multiple measurements.

Proper citation: IBD Detection Tool Benchmark Tool (RRID:SCR_022850) 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://pypi.org/

Software repository for Python programming language.Used to find and install software developed and shared by Python community.

Proper citation: PyPI (RRID:SCR_023145) Copy   

•   Source: SciCrunch Registry
  

http://cns.hkbu.edu.hk/RIDE.htm

Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials.

Proper citation: Residue Iteration Decomposition (RRID:SCR_022174) Copy   

•   Source: SciCrunch Registry
  

https://jarvis-mocap.github.io/jarvis-docs/

Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion.

Proper citation: Joint Acquisition, Recording and Voxel based Inference System (RRID:SCR_022723) 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://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
  

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

Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models.

Proper citation: ordinal (RRID:SCR_022856) Copy   

•   Source: SciCrunch Registry