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 (3.21)

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] (ORCID: ), 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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Sequencing, Software, VariantAnnotation, VariantDetection
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	MIT + file LICENSE
Depends
Imports	VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils
System Requirements
URL	https://github.com/BiodataAnalysisGroup/lineagespot
Bug Reports	https://github.com/BiodataAnalysisGroup/lineagespot/issues

Suggests	BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	lineagespot_1.11.0.tar.gz
Windows Binary (x86_64)	lineagespot_1.11.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
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