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https://cran.r-project.org/web/packages/biwt/index.html
Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator.
Proper citation: biwt (RRID:SCR_024271) Copy
https://cran.r-project.org/web/packages/Epi/index.html
Software R package provides functions for demographic and epidemiological analysis in Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and function for interval censored data and some useful functions for tabulation and plotting, as well as number of epidemiological data sets.
Proper citation: Epi (RRID:SCR_024272) Copy
https://sourceforge.net/projects/parsinsert/
Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.
Proper citation: ParsInsert (RRID:SCR_024163) 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
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://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
https://psignifit.sourceforge.net/
Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.
Proper citation: psignifit (RRID:SCR_024196) Copy
https://github.com/khowe/quicktree/
Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.
Proper citation: quicktree (RRID:SCR_024205) Copy
https://github.com/biod/sambamba
Software tools for working with SAM/BAM data
Proper citation: sambamba (RRID:SCR_024328) Copy
https://bioconductor.org/packages/release/bioc/html/annotate.html
Software R package for using R enviroments for annotation.
Proper citation: annotate (RRID:SCR_024221) 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://bioconductor.org/packages/release/bioc/html/affyio.html
Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats.
Proper citation: affyio (RRID:SCR_024223) Copy
https://bioconductor.org/packages/release/bioc/html/altcdfenvs.html
Software R package contains convenience data structures and functions to handle cdfenvs.
Proper citation: altcdfenvs (RRID:SCR_024225) 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=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://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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