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https://bioconductor.org/packages/release/bioc/html/biomformat.html

Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file.

Proper citation: biomformat (RRID:SCR_024228) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/biovizBase.html

Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization.

Proper citation: biovizBase (RRID:SCR_024229) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/GO.db.html

Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO.

Proper citation: go.db (RRID:SCR_024241) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/impute/

Software R package for imputation for microarray data.

Proper citation: impute (RRID:SCR_024243) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/Mergeomics/

Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts.

Proper citation: mergeomics (RRID:SCR_024244) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/metagenomeSeq/

Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations.

Proper citation: metagenomeseq (RRID:SCR_024246) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/biod/sambamba

Software tools for working with SAM/BAM data

Proper citation: sambamba (RRID:SCR_024328) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry