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lineagespot

Ιdentify and assign different SARS-CoV-2 lineages based on a single VCF file

https://github.com/biodataanalysisgroup/lineagespot

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.7%) to scientific vocabulary

Keywords from Contributors

bioconductor clonotype
Last synced: 11 months ago · JSON representation

Repository

Ιdentify and assign different SARS-CoV-2 lineages based on a single VCF file

Basic Info
  • Host: GitHub
  • Owner: BiodataAnalysisGroup
  • License: mit
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 22.2 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Fork of npechl/lineagespot
Created almost 5 years ago · Last pushed over 3 years ago

https://github.com/BiodataAnalysisGroup/lineagespot/blob/master/ 

# lineagespot


Lineagespot is a framework written in [R](https://www.r-project.org/), 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](https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format)). 


## Installation

```r
# install.packages("devtools")
devtools::install_github("BiodataAnalysisGroup/lineagespot")
```

## Raw data analysis

The processing steps of the raw fastq files can be found [here](inst/scripts/raw-data-analysis.md).

## Citation

If you use the tool, please cite the following work:

Pechlivanis, N., Tsagiopoulou, M., Maniou, M.C. et al. _Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece._ Sci Rep 12, 2659 (2022). https://doi.org/10.1038/s41598-022-06625-6

Owner

  • Name: Biodata Analysis Group
  • Login: BiodataAnalysisGroup
  • Kind: organization
  • Email: fpsom@certh.gr

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 142
  • Total Committers: 9
  • Avg Commits per committer: 15.778
  • Development Distribution Score (DDS): 0.423
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
nikopech n****1@g****m 82
Aspasia Orfanou a****r@h****m 13
iofeidis j****5@g****m 10
mcmaniou m****u@y****r 10
Sofoklis Keisaris 8****5 10
tatsistog t****a@e****r 8
Stella 7****l 5
Fotis E. Psomopoulos f****m@g****m 2
Aspasia Orfanou 4****r 2
Committer Domains (Top 20 + Academic)
ece.auth.gr: 1 yahoo.gr: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 2
  • Total pull requests: 5
  • Average time to close issues: 15 minutes
  • Average time to close pull requests: 3 minutes
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • npechl (1)
  • aspaor (1)
Pull Request Authors
  • npechl (5)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 5,730 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: lineagespot

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

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5,730 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 19.8%
Stargazers count: 24.9%
Average: 27.6%
Downloads: 93.5%
Maintainers (1)
inab.bioinformatics@lists.certh.gr
Last synced: 12 months ago