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https://github.com/denglab/SeqSero
Software pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.
Proper citation: seqsero (RRID:SCR_024333) Copy
https://cran.r-project.org/package=RNeXML
Software R package provides access to phyloinformatic data in 'NeXML' format.
Proper citation: rnexml (RRID:SCR_024291) Copy
https://cran.r-project.org/package=phylobase
Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis.
Proper citation: phylobase (RRID:SCR_024292) Copy
https://cran.r-project.org/web/packages/qqman/index.html
Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files.
Proper citation: qqman (RRID:SCR_024293) Copy
https://synonym.caltech.edu/software/sbmltoolbox/
Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave.
Proper citation: sbmltoolbox (RRID:SCR_024329) Copy
https://cran.r-project.org/package=tigger
Software R package infers V genotype of individual from immunoglobulin repertoire sequencing data like AIRR-Seq, Rep-Seq. Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among sample sequences.
Proper citation: tigger (RRID:SCR_024310) Copy
https://cran.r-project.org/package=wavethresh
Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
Proper citation: wavethresh (RRID:SCR_024311) Copy
https://cran.r-project.org/package=WebGestaltR
Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results.
Proper citation: webgestaltr (RRID:SCR_024312) Copy
https://cran.r-project.org/web/packages/sjPlot/index.html
Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data.
Proper citation: sjplot (RRID:SCR_024307) Copy
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
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
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
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
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
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
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
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
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
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
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
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