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http://www.bioconductor.org/

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Proper citation: Bioconductor (RRID:SCR_006442) Copy   

•   Source: SciCrunch Registry

http://www.rhino3d.com/features

3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products.

Proper citation: Rhinoceros (RRID:SCR_014339) Copy   

•   Source: SciCrunch Registry

https://web.stanford.edu/group/pritchardlab/structure.html

Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms.

Proper citation: STRUCTURE (RRID:SCR_017637) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/argus/

Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.

Proper citation: Argus (RRID:SCR_021585) Copy   

•   Source: SciCrunch Registry

https://www.syngene.com/software/genetools-automatic-image-analysis/

Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.

Proper citation: GeneTools (RRID:SCR_022505) Copy   

•   Source: SciCrunch Registry

http://www.hkl-xray.com/hkl-2000

Software package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions.

Proper citation: HKL-2000 (RRID:SCR_015547) Copy   

•   Source: SciCrunch Registry

http://www.sigmaplot.com/products/sigmaplot/

Statistical analysis and scientific graphing software for Windows OS.

Proper citation: SigmaPlot (RRID:SCR_003210) Copy   

•   Source: SciCrunch Registry

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

Software R package provides risk regression models and prediction scores for survival analysis with competing risks.

Proper citation: riskRegression (RRID:SCR_024424) Copy   

•   Source: SciCrunch Registry

https://github.com/SouthGreenPlatform/rap-green

Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package.

Proper citation: RapGreen (RRID:SCR_024426) Copy   

•   Source: SciCrunch Registry

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

Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot.

Proper citation: ROCit (RRID:SCR_024420) Copy   

•   Source: SciCrunch Registry

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

Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats.

Proper citation: Rgdal (RRID:SCR_024422) Copy   

•   Source: SciCrunch Registry

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

Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data.

Proper citation: survivalROC (RRID:SCR_024415) Copy   

•   Source: SciCrunch Registry

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

Software R package enables creation of Ridgeline plots in 'ggplot2'

Proper citation: ggridges (RRID:SCR_024511) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gamm4

Software R package to estimate generalized additive mixed models.

Proper citation: gamm4 (RRID:SCR_024507) Copy   

•   Source: SciCrunch Registry

https://ice.synthego.com/#/

Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data.

Proper citation: Inference of CRISPR Edits (RRID:SCR_024508) Copy   

•   Source: SciCrunch Registry

https://www.mathworks.com/products/optimization.html

Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations.

Proper citation: Optimization Toolbox (RRID:SCR_024486) Copy   

•   Source: SciCrunch Registry

https://github.com/navinlabcode/copykat

Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data.

Proper citation: CopyKAT (RRID:SCR_024512) Copy   

•   Source: SciCrunch Registry

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

Software R package for choosing univariate class intervals for mapping or other graphics purposes.

Proper citation: classInt (RRID:SCR_024515) Copy   

•   Source: SciCrunch Registry

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

Software R package for multiple imputation of missing data in multilevel modeling.

Proper citation: mitml (RRID:SCR_024516) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.

Proper citation: BLASTP (RRID:SCR_001010) Copy   

•   Source: SciCrunch Registry