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lineagespot
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see lineagespot.
Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Bioconductor version: 3.18
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 lists.certh.gr>
citation("lineagespot")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lineagespot")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("lineagespot")
Details
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Follow Installation instructions to use this package in your R session.