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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://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://sourceforge.net/projects/trinculo/

Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.

Proper citation: Trinculo (RRID:SCR_024384) Copy   

•   Source: SciCrunch Registry

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

Software R package provides environment for Time-Frequency analysis of 1-D signals.

Proper citation: rwave (RRID:SCR_024302) Copy   

•   Source: SciCrunch Registry

https://github.com/vals/umis

Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.

Proper citation: umis (RRID:SCR_024381) Copy   

•   Source: SciCrunch Registry

https://github.com/ncbi/sra-tools/

Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.

Proper citation: sra-toolkit (RRID:SCR_024350) Copy   

•   Source: SciCrunch Registry

http://gwyddion.net/

Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.

Proper citation: Gwyddion (RRID:SCR_015583) Copy   

•   Source: SciCrunch Registry

https://github.com/mikelove/tximport

Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.

Proper citation: tximport (RRID:SCR_016752) Copy   

•   Source: SciCrunch Registry

https://github.com/ANGSD/ngsRelate

Software tool for estimating pairwise relatedness from next-generation sequencing data.

Proper citation: ngsRelate (RRID:SCR_016588) Copy   

•   Source: SciCrunch Registry