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https://bioconductor.org/packages/Gviz/
Software R package to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package.
Proper citation: gviz (RRID:SCR_024239) Copy
https://cran.r-project.org/package=psychometric
Software R package for measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, and correlation
Proper citation: psychometric (RRID:SCR_024295) Copy
https://rniftilib.r-forge.r-project.org/
Software R package provides R-interface to the NIfTI reference implementation the niftilib C-library.
Proper citation: rniftilib (RRID:SCR_024296) Copy
https://cran.r-project.org/package=Rook
Web server for R with documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications.
Proper citation: rook (RRID:SCR_024298) Copy
https://cran.r-project.org/package=RobustRankAggreg
Software R package for aggregating ranked lists, especially lists of genes. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.
Proper citation: robustrankaggreg (RRID:SCR_024299) Copy
https://cran.r-project.org/package=rncl
Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.
Proper citation: rncl (RRID:SCR_024290) Copy
https://cran.r-project.org/web/packages/hms/index.html
Software R package implements S3 class for storing and formatting time-of-day values, based on the 'difftime' class.
Proper citation: hms (RRID:SCR_024294) Copy
https://github.com/biod/sambamba
Software tools for working with SAM/BAM data
Proper citation: sambamba (RRID:SCR_024328) Copy
https://gitlab.com/chrjan/seq-seq-pan
Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment.
Proper citation: seq-seq-pan (RRID:SCR_024343) Copy
https://cran.r-project.org/web/packages/epibasix/index.html
Software R package for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement.
Proper citation: epibasix (RRID:SCR_024275) Copy
https://cran.r-project.org/web/packages/incidence/index.html
Software R package provides functions and classes to compute, handle and visualise incidence from dated events for defined time interval. Dates can be provided in various standard formats.
Proper citation: incidence (RRID:SCR_024276) Copy
https://cran.r-project.org/web/packages/genetics/index.html
Software R package for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium.
Proper citation: genetics (RRID:SCR_024279) Copy
https://github.com/rdpstaff/ReadSeq
Software package as Java based common sequence file format reader and sequence file manipulation.
Proper citation: readseq (RRID:SCR_024313) Copy
https://cran.r-project.org/package=rsvd
Software R package used to compute near optimal low-rank singular value decomposition of massive data sets with high accuracy. Provides several randomized matrix algorithms such as randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided.
Proper citation: rsvd (RRID:SCR_024303) Copy
https://cran.r-project.org/package=surveillance
Software R package for modeling and monitoring of time series of counts, proportions and categorical data, as well as for modeling of continuous-time point processes of epidemic phenomena.
Proper citation: surveillance (RRID:SCR_024304) Copy
https://cran.r-project.org/package=tsne
Softare R package as implementation of the t-SNE algorithm.
Proper citation: tsne (RRID:SCR_024305) Copy
https://cran.r-project.org/web/packages/Rook/index.html
Software R package provides interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling comprehensive phylogenetic tree for all named species.
Proper citation: rotl (RRID:SCR_024306) Copy
https://cran.r-project.org/web/packages/snowfall/index.html
Software R package usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.
Proper citation: snowfall (RRID:SCR_024309) Copy
https://cran.r-project.org/package=parmigene
Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks.
Proper citation: parmigene (RRID:SCR_024285) Copy
https://cran.r-project.org/web/packages/pcaPP/index.html
Software R package provides functions for principal component analysis by projection pursuit.
Proper citation: pcapp (RRID:SCR_024287) Copy
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