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

Software R package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3).

Proper citation: rann (RRID:SCR_024297) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software R package to scrape data from Fitbit to generate graphs.

Proper citation: fitbitscraper (RRID:SCR_024273) Copy   

•   Source: SciCrunch Registry

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

Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.

Proper citation: fitdistrplus (RRID:SCR_024274) Copy   

•   Source: SciCrunch Registry

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

Software R package for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.

Proper citation: forecast (RRID:SCR_024277) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software R package as implementation of LexRank algorithm. Used for computing sentence importance based on concept of eigenvector centrality in graph representation of sentences.

Proper citation: lexrankr (RRID:SCR_024278) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package.

Proper citation: DT (RRID:SCR_024270) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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