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https://cran.r-project.org/web/packages/epibasix/index.html
Software R package for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement.
Proper citation: epibasix (RRID:SCR_024275) Copy
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.
Proper citation: PDB2PQR (RRID:SCR_024155) Copy
https://cran.r-project.org/web/packages/incidence/index.html
Software R package provides functions and classes to compute, handle and visualise incidence from dated events for defined time interval. Dates can be provided in various standard formats.
Proper citation: incidence (RRID:SCR_024276) Copy
https://github.com/sib-swiss/pftools3
Software suite of tools to build and search generalized profiles.
Proper citation: PfTools (RRID:SCR_024158) 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://jydu.github.io/physamp/
Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.
Proper citation: PhySamp (RRID:SCR_024159) Copy
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
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