DOI: 10.18129/B9.bioc.lineagespot    

This is the development version of lineagespot; for the stable release version, see lineagespot.

Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

Bioconductor version: Development (3.17)

Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.

Author: Nikolaos Pechlivanis [aut, cre] , Maria Tsagiopoulou [aut], Maria Christina Maniou [aut], Anastasis Togkousidis [aut], Evangelia Mouchtaropoulou [aut], Taxiarchis Chassalevris [aut], Serafeim Chaintoutis [aut], Chrysostomos Dovas [aut], Maria Petala [aut], Margaritis Kostoglou [aut], Thodoris Karapantsios [aut], Stamatia Laidou [aut], Elisavet Vlachonikola [aut], Aspasia Orfanou [aut], Styliani-Christina Fragkouli [aut], Sofoklis Keisaris [aut], Anastasia Chatzidimitriou [aut], Agis Papadopoulos [aut], Nikolaos Papaioannou [aut], Anagnostis Argiriou [aut], Fotis E. Psomopoulos [aut]

Maintainer: Nikolaos Pechlivanis <inab.bioinformatics at>

Citation (from within R, enter citation("lineagespot")):


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biocViews Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.3.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 years)
License MIT + file LICENSE
Imports VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils
Suggests BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0)
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