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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

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   

•   Source: SciCrunch Registry

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

Softare R package as implementation of the t-SNE algorithm.

Proper citation: tsne (RRID:SCR_024305) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.

Proper citation: psychotree (RRID:SCR_024288) Copy   

•   Source: SciCrunch Registry

http://saint-apms.sourceforge.net/Main.html

Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: saint (RRID:SCR_024324) Copy   

•   Source: SciCrunch Registry

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

Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.

Proper citation: dynamicTreeCut (RRID:SCR_024280) Copy   

•   Source: SciCrunch Registry

https://github.com/artic-network/readucks

Software package as Nanopore read de-multiplexer.

Proper citation: readucks (RRID:SCR_024315) Copy   

•   Source: SciCrunch Registry

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

Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.

Proper citation: stringi (RRID:SCR_024319) Copy   

•   Source: SciCrunch Registry

http://varna.lri.fr/

Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.

Proper citation: VARNA (RRID:SCR_024373) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/preprocessCore/

Software library of core preprocessing routines.

Proper citation: preprocesscore (RRID:SCR_024254) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/qusage/

Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies.

Proper citation: qusage (RRID:SCR_024255) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/Rsamtools/

Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files.

Proper citation: rsamtools (RRID:SCR_024257) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/savR/

Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots.

Proper citation: savr (RRID:SCR_024258) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/NanoStringQCPro/

Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output.

Proper citation: nanostringqcpro (RRID:SCR_024250) Copy   

•   Source: SciCrunch Registry

https://github.com/vgteam/vg#vg

Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.

Proper citation: variation graph (RRID:SCR_024369) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/PWMEnrich/

Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation.

Proper citation: pwmenrich (RRID:SCR_024249) Copy   

•   Source: SciCrunch Registry