lineagespot
This is the released version of lineagespot; for the devel version, see lineagespot.
Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | lineagespot_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | lineagespot_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | lineagespot_1.16.0.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 |