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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
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
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
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
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
https://github.com/artic-network/readucks
Software package as Nanopore read de-multiplexer.
Proper citation: readucks (RRID:SCR_024315) Copy
https://github.com/FunctionalUrology/MLme
Software toolkit for Machine Learning Driven Data Analysis. Simplifies machine learning for data exploration, visualization and analysis.
Proper citation: Machine Learning Made Easy (RRID:SCR_024439) Copy
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
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
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
https://cran.r-project.org/web/packages/bedr/vignettes/Using-bedr.html
Software R package for genomic interval processing.Genomic regions processing using open-source command line tools to perform genome arithmetic e.g indexing, formatting and merging.
Proper citation: bedr (RRID:SCR_024526) Copy
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
https://CRAN.R-project.org/package=ROCit
Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot.
Proper citation: ROCit (RRID:SCR_024420) Copy
https://zzz.bwh.harvard.edu/luna/
Software package for analysis of sleep signal data. Open source C/C++ software for manipulating and analyzing polysomnographic recordings, with focus on sleep EEG.
Proper citation: Luna (RRID:SCR_024541) Copy
https://CRAN.R-project.org/package=rgdal
Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats.
Proper citation: Rgdal (RRID:SCR_024422) Copy
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
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