Package: QSutils 1.23.0

Mercedes Guerrero-Murillo

QSutils: Quasispecies Diversity

Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.

Authors:Mercedes Guerrero-Murillo [cre, aut], Josep Gregori i Font [aut]

QSutils_1.23.0.tar.gz
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QSutils.pdf |QSutils.html✨
QSutils/json (API)
NEWS

# Install 'QSutils' in R:
install.packages('QSutils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:QSutils-1.23.0(bioc 3.20)QSutils-1.22.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

48 exports 1.58 score 27 dependencies 1 dependents 2 mentions

Last updated 2 months agofrom:52c3795966

Exports:CollapseConsSeqCorrectGapsAndNsDBruleDivergeDNA.distDottedAlignmentDSFTFADfn.abFreqMatGenerateVarsgeom.seriesGetInfProfileGetQSDataGetRandomSeqGiniSimpsonGiniSimpsonMVUEGiniSimpsonVarHCqHCqProfileHCqVarHillHillProfileIntersectStrandHplsMutationFreqMutationFreqVarMutsTblNormShannonNormShannonVarNucleotideDiversityPolyDistRaoRaoPowRaoPowProfileRaoVarReadAmplSeqsRecollapseRenyiRenyiProfileReportVariantsSegSitesShannonShannonVarSortByMutationsSummaryMutsTotalMutationsUniqueMutations

Dependencies:apeaskpassBiocGenericsBiostringscrayoncurldigestGenomeInfoDbGenomeInfoDbDataGPArotationhttrIRangesjsonlitelatticemimemnormtnlmeopensslpsychpwalignR6RcppS4VectorssysUCSC.utilsXVectorzlibbioc

Quasispecies Data

Guerrero-Murillo, M and Gregori, J

Rendered fromQSUtils-Alignment.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2018-10-18
Started: 2018-09-14

Characterizing viral quasispecies

Guerrero-Murillo, M and Gregori, J

Rendered fromQSutils-Diversity.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2018-10-18
Started: 2018-07-02

Simulating Quasispecies Composition

Guerrero-Murillo, M and Gregori, J

Rendered fromQSutils-Simulation.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2018-10-18
Started: 2018-06-28

Readme and manuals

Help Manual

Help pageTopics
Quasispecies DiversityQSutils-package QSutils
Collapse reads into haplotypes and frequenciesCollapse Recollapse
Consensus sequence given an alignment and frequenciesConsSeq
Function to correct an alignment with gaps and NsCorrectGapsAndNs
Genotyping by the DB ruleDBrule
Generate a set of diverging haplotypesDiverge
Matrix of DNA distances given an alignmentDNA.dist
Align haplotypes into a dotted alignmentDottedAlignment
Downsampling followed by fringe trimmingDSFT
Functional attribute diversityFAD
Vector of abundances with different methodsfn.ab
Matrix of nucleotide or amino acid frequencies in alignment by positionFreqMat
Generate variants of a given haplotypeGenerateVars
Genotype standards of hepatitis B virusGenotypeStandards_A-H.fas
Geometric seriesgeom.series
Information content profile of an alignmentGetInfProfile
Read the aligned sequences, filter at minimum abundance, and sort the sequencesGetQSData
Generate a random sequenceGetRandomSeq
Functions to calculate the GiniSimpson indexGiniSimpson GiniSimpsonMVUE GiniSimpsonVar
Set of functions to compute the Havrda-Charvat estimatorHCq HCqProfile HCqVar
Hill numbersHill HillProfile
Forward and reverse strand haplotype intersectionsIntersectStrandHpls
Mutation frequency with respect to the dominant haplotypeMutationFreq MutationFreqVar
Table of mutation frequencies by positionMutsTbl
Nucleotide diversityNucleotideDiversity
Fraction of substitutions by polymorphic sitePolyDist
Functions to compute Rao’s entropyRao RaoPow RaoPowProfile RaoVar
Read a fasta file with haplotypes and frequenciesReadAmplSeqs
Rényi profilesRenyi RenyiProfile
Report variantsReportVariants
Compute the number of segregating sitesSegSites
Set of functions to compute Shannon entropyNormShannon NormShannonVar Shannon ShannonVar
Sort haplotypes by mutations and abundanceSortByMutations
Distribution of nucleotides or amino acids in polymorphic sitesSummaryMuts
Number of MutationsTotalMutations
Fasta file with raw reads with gaps and NsToy.GapsAndNs.fna
Fasta file with 10 haplotypes, 50 basepairs in size.ToyData_10_50_1000.fna
Fasta file with forward readsToyData_FWReads.fna
Fasta file with reverse reads.ToyData_RVReads.fna
Number of unique mutationsUniqueMutations
Fasta file with reads of unknown genotypeUnknown-Genotype.fna