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Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes.
Proper citation: CARD (RRID:SCR_023995) Copy
https://www.tau.ac.il/~itaymay/cp/rate4site.html
Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins.
Proper citation: Rate4Site (RRID:SCR_024222) Copy
http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/
Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.
Proper citation: ChromImpute (RRID:SCR_023990) Copy
https://github.com/HadrienG/InSilicoSeq
Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
Proper citation: InSilicoSeq (RRID:SCR_024041) Copy
https://github.com/fccoelho/epigrass
Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.
Proper citation: Epigrass (RRID:SCR_024016) Copy
https://github.com/jnktsj/DNApi/
Software de novo adapter prediction algorithm for small RNA sequencing data.
Proper citation: DNApi (RRID:SCR_024009) Copy
https://www.sofa-framework.org/
Open source software framework targeting at real-time simulation, with emphasis on medical simulation.
Proper citation: sofa-apps (RRID:SCR_024346) Copy
https://sourceforge.net/projects/surankco/
Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.
Proper citation: surankco (RRID:SCR_024355) Copy
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
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/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
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/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
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
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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