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https://cran.r-project.org/package=waveslim

Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis.

Proper citation: waveslim (RRID:SCR_024308) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/NMF/index.html

Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

Proper citation: nmf (RRID:SCR_024284) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=pROC

Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

Proper citation: proc (RRID:SCR_024286) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=psyphy

Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations.

Proper citation: psyphy (RRID:SCR_024289) Copy   

•   Source: SciCrunch Registry

https://bioruby.org/

Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

Proper citation: ruby-bio (RRID:SCR_024322) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/Mediana/index.html

Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria.

Proper citation: mediana (RRID:SCR_024281) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/itertools/index.html

Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package.

Proper citation: itertools (RRID:SCR_024282) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/OptimalCutpoints/index.html

Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.

Proper citation: optimalcutpoints (RRID:SCR_024283) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rpact/index.html

Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints.

Proper citation: rpact (RRID:SCR_024300) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/shazam/index.html

Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.

Proper citation: shazam (RRID:SCR_024301) Copy   

•   Source: SciCrunch Registry

https://github.com/rrwick/Unicycler

Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.

Proper citation: Unicycler (RRID:SCR_024380) Copy   

•   Source: SciCrunch Registry

http://tab2mage.sourceforge.net/

Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database.

Proper citation: tab2mage (RRID:SCR_024359) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

•   Source: SciCrunch Registry

https://github.com/pybel

Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.

Proper citation: PyBEL (RRID:SCR_017660) Copy   

•   Source: SciCrunch Registry

https://code.google.com/archive/p/kempbasu/

Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts.

Proper citation: kempbasu (RRID:SCR_024055) Copy   

•   Source: SciCrunch Registry

http://www.bioimagexd.net/

Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once.

Proper citation: BioImageXD (RRID:SCR_023979) Copy   

•   Source: SciCrunch Registry

http://www.bali-phy.org

Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.

Proper citation: BAli-Phy (RRID:SCR_023976) Copy   

•   Source: SciCrunch Registry

https://github.com/intake/intake

Software package for finding, investigating, loading and disseminating data.

Proper citation: Intake (RRID:SCR_024042) Copy   

•   Source: SciCrunch Registry

https://github.com/andersen-lab/ivar

Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.

Proper citation: iVar (RRID:SCR_024045) Copy   

•   Source: SciCrunch Registry

https://changeo.readthedocs.io

Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences.

Proper citation: Change-O (RRID:SCR_023986) Copy   

•   Source: SciCrunch Registry