Package: lineagespot 1.9.0

Nikolaos Pechlivanis

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

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.

Authors: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]

lineagespot_1.9.0.tar.gz
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lineagespot.pdf |lineagespot.html✨
lineagespot/json (API)
NEWS

# Install 'lineagespot' in R:

install.packages('lineagespot', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biodataanalysisgroup/lineagespot/issues

On BioConductor:lineagespot-1.9.0(bioc 3.20)lineagespot-1.8.0(bioc 3.19)

bioconductor-package

8 exports 1.16 score 74 dependencies

Last updated 2 months agofrom:ae4993ee5b

Exports:get_lineage_report is_gff3 lineagespot lineagespot_hits list_input list_vcf merge_vcf uniq_variants

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl data.table DBI DelayedArray fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys UCSC.utils VariantAnnotation vctrs XML XVector yaml zlibbioc

lineagespot User Guide

Nikolaos Pechlivanis, Maria Tsagiopoulou, Maria Christina Maniou, Anastasis Togkousidis, Evangelia Mouchtaropoulou, Taxiarchis Chassalevris, Serafeim Chaintoutis, Chrysostomos Dovas, Maria Petala, Margaritis Kostoglou, Thodoris Karapantsios, Stamatia Laidou, Elisavet Vlachonikola, Anastasia Chatzidimitriou, Agis Papadopoulos, Nikolaos Papaioannou, Anagnostis Argiriou, Fotis E. Psomopoulos

Rendered fromlineagespot.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-01-12
Started: 2021-09-17

Help page	Topics
get_lineage_report	get_lineage_report
is_gff3	is_gff3
lineagespot	lineagespot
lineagespot_hits	lineagespot_hits
list_input	list_input
list_vcf	list_vcf
merge_vcf	merge_vcf
uniq_variants	uniq_variants

Package: lineagespot 1.9.0

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

lineagespot User Guide

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)