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https://whonet.org/

Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide.

Proper citation: WHONET (RRID:SCR_024495) Copy   

•   Source: SciCrunch Registry

https://www.certara.com/software/phoenix-pkpd/

Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.

Proper citation: WinNonlin (RRID:SCR_024504) Copy   

•   Source: SciCrunch Registry

https://github.com/harvardinformatics/NGmerge

Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates.

Proper citation: NGmerge (RRID:SCR_024483) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/alien_hunter/

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.

Proper citation: Alien hunter (RRID:SCR_004575) Copy   

•   Source: SciCrunch Registry

https://github.com/chaoszhang/A-pro

Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.

Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/paulgeeleher/pRRophetic

Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,

Proper citation: pRRophetic (RRID:SCR_024417) 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://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://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