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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms.
Proper citation: Thermo Scientific Maps Software (RRID:SCR_024446) 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://github.com/losonczylab/sima
Software Python package for analysis of dynamic fluorescence microscopy data.
Proper citation: SIMA (RRID:SCR_024466) Copy
https://bioconductor.org/packages/microbiome/
Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data.
Proper citation: microbiome (RRID:SCR_024699) 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://samuel-marsh.github.io/scCustomize/
Software R package for custom visualizations and functions for streamlined analyses of single cell sequencing.
Proper citation: scCustomize (RRID:SCR_024675) 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=riskRegression
Software R package provides risk regression models and prediction scores for survival analysis with competing risks.
Proper citation: riskRegression (RRID:SCR_024424) 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://github.com/SouthGreenPlatform/rap-green
Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package.
Proper citation: RapGreen (RRID:SCR_024426) 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
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