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https://github.com/helioalexandre/MouBeAT
Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM).
Proper citation: Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) Copy
https://CRAN.R-project.org/package=vcfR
Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data.
Proper citation: vcfR (RRID:SCR_023453) Copy
https://grunwaldlab.github.io/poppr/
Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction.
Proper citation: poppr (RRID:SCR_023452) Copy
https://CRAN.R-project.org/package=irrCAC
Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses.
Proper citation: Computing Chance Corrected Agreement Coefficients (RRID:SCR_023176) Copy
https://CRAN.R-project.org/package=irrICC
Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability.
Proper citation: Intraclass Correlations for Quantifying Inter Rater Reliability (RRID:SCR_023175) Copy
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
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
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
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
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
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
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
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
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
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
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
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
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
https://bioconductor.org/packages/org.Mm.eg.db/
Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers.
Proper citation: org.Mm.eg.db (RRID:SCR_023488) Copy
https://github.com/Shenhav-and-Korem-labs/SCRuB
Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program.
Proper citation: SCRuB (RRID:SCR_023518) Copy
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