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lineagespot

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

Bioconductor version: Release (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 lists.certh.gr>

Citation (from within R, enter 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")
lineagespot User Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends
Imports VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils
Linking To
Suggests BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/BiodataAnalysisGroup/lineagespot
Bug Reports https://github.com/BiodataAnalysisGroup/lineagespot/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package lineagespot_1.4.0.tar.gz
Windows Binary lineagespot_1.4.0.zip
macOS Binary (x86_64) lineagespot_1.4.0.tgz
macOS Binary (arm64) lineagespot_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lineagespot
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lineagespot
Bioc Package Browser https://code.bioconductor.org/browse/lineagespot/
Package Short Url https://bioconductor.org/packages/lineagespot/
Package Downloads Report Download Stats