lineagespot
Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Bioconductor version: Release (3.19)
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 "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 1.8.0 |
| 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 |
See More
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | lineagespot_1.8.0.zip |
| macOS Binary (x86_64) | lineagespot_1.8.0.tgz |
| macOS Binary (arm64) | lineagespot_1.8.0.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 |