lineagespot
Bioc currentDetection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
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.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
14 8 exported
Complexity
3.1 avg / 12 max
Call network
14 nodes / 8 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
1,822
Files
49
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
6
Testing & CI
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-04-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Nikolaos Pechlivanis author maintainer
- Anagnostis Argiriou author
- Serafeim Chaintoutis author
- Taxiarchis Chassalevris author
- Anastasia Chatzidimitriou author
- Chrysostomos Dovas author
- Styliani-Christina Fragkouli author
- Thodoris Karapantsios author
- Sofoklis Keisaris author
- Margaritis Kostoglou author
- Stamatia Laidou author
- Maria Christina Maniou author
- Evangelia Mouchtaropoulou author
- Aspasia Orfanou author
- Agis Papadopoulos author
- Nikolaos Papaioannou author
- Maria Petala author
- Fotis E. Psomopoulos author
- Anastasis Togkousidis author
- Maria Tsagiopoulou author
- Elisavet Vlachonikola author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("lineagespot")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.