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https://cab.spbu.ru/software/spades/
Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SPAdes (RRID:SCR_000131) Copy
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
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
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
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
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
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
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
https://CRAN.R-project.org/package=ggridges
Software R package enables creation of Ridgeline plots in 'ggplot2'
Proper citation: ggridges (RRID:SCR_024511) Copy
https://CRAN.R-project.org/package=gamm4
Software R package to estimate generalized additive mixed models.
Proper citation: gamm4 (RRID:SCR_024507) Copy
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
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
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
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
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
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
http://www.drive5.com/muscle/prefab.htm
Downloadable data designed for testing multiple sequence alignment methods.
Proper citation: PREFAB (RRID:SCR_001009) Copy
http://www.mutationtaster.org/
Evaluates disease-causing potential of sequence alterations.
Proper citation: MutationTaster (RRID:SCR_010777) Copy
http://www.ebi.ac.uk/Tools/sss/wublast/
Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity.
Proper citation: WU-BLAST (RRID:SCR_011824) Copy
http://www.helsinki.fi/~tsjuntun/linkage/analyze/
A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software)
Proper citation: ANALYZE (RRID:SCR_009120) Copy
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