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

Software R package Themes for use with Shiny.

Proper citation: shinythemes (RRID:SCR_022757) Copy   

•   Source: SciCrunch Registry

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://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://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://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://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://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

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/tlancian/bio_cs

Software package for implementing algorithms proposed in Lanciano et al. "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data".

Proper citation: bio_contrast_subgraph (RRID:SCR_022853) Copy   

•   Source: SciCrunch Registry

https://github.com/HChai01/ISGPRE

Software package for predicting interferon stimulated human genes.

Proper citation: ISGPRE (RRID:SCR_022730) Copy   

•   Source: SciCrunch Registry