syntenet

An R package to infer and analyze synteny networks from protein sequences

https://github.com/almeidasilvaf/syntenet

Science Score: 36.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
✓
DOI references
Found 2 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
2 of 4 committers (50.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (17.2%) to scientific vocabulary

Keywords

comparative-genomics evolutionary-genomics network-science phylogenomics rstats synteny synteny-network

Keywords from Contributors

bioconductor-packages gene grna-sequence immune-repertoire bioinformatics genomics sequencing ontologies

Last synced: 6 months ago · JSON representation

Repository

An R package to infer and analyze synteny networks from protein sequences

Basic Info

Host: GitHub
Owner: almeidasilvaf
Language: R
Default Branch: devel
Homepage: https://almeidasilvaf.github.io/syntenet/
Size: 78 MB

Statistics

Stars: 30
Watchers: 3
Forks: 6
Open Issues: 0
Releases: 0

Topics

comparative-genomics evolutionary-genomics network-science phylogenomics rstats synteny synteny-network

Created almost 4 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Code of conduct Support

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# syntenet 


[![GitHub issues](https://img.shields.io/github/issues/almeidasilvaf/syntenet)](https://github.com/almeidasilvaf/syntenet/issues)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![R-CMD-check-bioc](https://github.com/almeidasilvaf/syntenet/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/almeidasilvaf/syntenet/actions)
[![Codecov test
coverage](https://codecov.io/gh/almeidasilvaf/syntenet/branch/devel/graph/badge.svg)](https://codecov.io/gh/almeidasilvaf/syntenet?branch=devel)


The goal of `syntenet` is to infer synteny networks from whole-genome 
protein sequence data and analyze them. Anchor pairs from synteny analyses are
treated as an undirected unweighted graph (i.e., a synteny network),
and users can perform: 

- **Synteny detection** using a native implementation of the 
[MCScanX algorithm](https://doi.org/10.1093/nar/gkr1293), a C++ program that 
has been modified and ported to R with Rcpp. This way, users do not need to 
install MCScanX beforehand, because `syntenet` has its own implementation
of the same algorithm.
- **Synteny network inference** by treating anchor pairs as edges of a graph;
- **Network clustering** using the Infomap algorithm;
- **Phylogenomic profiling**, which consists in identifying which species 
contain which clusters. This analysis can reveal highly conserved synteny
clusters and taxon-specific ones (e.g., family- and order-specific clusters); 
- **Microsynteny-based phylogeny reconstruction** with maximum likelihood,
which can be achieved by inferring a phylogeny from a binary matrix of
phylogenomic profiles with IQTREE.


## Installation instructions

Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `syntenet` from [Bioconductor](http://bioconductor.org/) using the following code:

```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("syntenet")
```

And the development version from [GitHub](https://github.com/almeidasilvaf/syntenet) with:

```{r 'install_dev', eval = FALSE}
BiocManager::install("almeidasilvaf/syntenet")
```

## Citation

Below is the citation output from using `citation('syntenet')` in R. Please
run this yourself to check for any updates on how to cite __syntenet__.

```{r 'citation', eval = requireNamespace('syntenet')}
print(citation('syntenet'), bibtex = TRUE)
```

Please note that `syntenet` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

## Code of Conduct

Please note that the `syntenet` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.

## Development tools

* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://almeidasilvaf.github.io/syntenet) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.

For more details, check the `dev` directory.

This package was developed using `r BiocStyle::Biocpkg('biocthis')`.

Owner

Name: Fabrício Almeida-Silva
Login: almeidasilvaf
Kind: user
Location: Technologiepark 71, Ghent, Belgium
Company: VIB-UGent Center for Plant Systems Biology

Website: https://almeidasilvaf.github.io
Twitter: almeidasilvaf
Repositories: 7
Profile: https://github.com/almeidasilvaf

Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.

GitHub Events

Total

Issues event: 8
Watch event: 6
Issue comment event: 9
Push event: 6
Create event: 2

Last Year

Issues event: 8
Watch event: 6
Issue comment event: 9
Push event: 6
Create event: 2

Committers

Last synced: over 2 years ago

All Time

Total Commits: 116
Total Committers: 4
Avg Commits per committer: 29.0
Development Distribution Score (DDS): 0.353

Past Year

Commits: 56
Committers: 4
Avg Commits per committer: 14.0
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
almeidasilvaf	f**a@h**m	75
Kristian Ullrich	u**h@e**e	37
J Wokaty	j**y@s**u	2
J Wokaty	j****y	2

Committer Domains (Top 20 + Academic)

sph.cuny.edu: 1 evolbio.mpg.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 21
Total pull requests: 7
Average time to close issues: 5 days
Average time to close pull requests: 1 day
Total issue authors: 13
Total pull request authors: 1
Average comments per issue: 4.05
Average comments per pull request: 0.43
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 6
Pull requests: 0
Average time to close issues: 7 days
Average time to close pull requests: N/A
Issue authors: 5
Pull request authors: 0
Average comments per issue: 1.5
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

dmacguigan (4)
alexvasilikop (3)
sujee119 (2)
WWz33 (2)
jhcuarta (1)
shun-oit (1)
enriquepola1996 (1)
iaindhay (1)
aurelim (1)
SJ-Smit (1)
xiaoyezao (1)
YingChen94 (1)
PeterMulhair (1)

Pull Request Authors

kullrich (7)

Top Labels

Issue Labels

enhancement (2) documentation (1) bug (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 8,311 total

Total dependent packages: 1
Total dependent repositories: 0
Total versions: 9
Total maintainers: 1

bioconductor.org: syntenet

Inference And Analysis Of Synteny Networks

Homepage: https://github.com/almeidasilvaf/syntenet
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/syntenet/inst/doc/syntenet.pdf
License: GPL-3
Latest release: 1.10.2
published 6 months ago

Versions: 9
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 8,311 Total

Rankings

Dependent repos count: 0.0%

Forks count: 8.8%

Stargazers count: 9.1%

Dependent packages count: 19.9%

Average: 25.6%

Downloads: 90.0%

Maintainers (1)

fabricio_almeidasilva@hotmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 4.2 depends
Biostrings * imports
GenomicRanges * imports
RColorBrewer * imports
Rcpp >= 1.0.8 imports
ggnetwork * imports
ggplot2 * imports
grDevices * imports
igraph * imports
intergraph * imports
methods * imports
networkD3 * imports
pheatmap * imports
stats * imports
utils * imports
vegan * imports
BiocStyle * suggests
covr * suggests
ggtree * suggests
knitr * suggests
rmarkdown * suggests
testthat >= 3.0.0 suggests
xml2 * suggests

.github/workflows/check-bioc.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact v2 composite
docker/build-push-action v1 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

ecosyste.ms

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Experiments

Open Source Science

syntenet

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

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Topics

Metadata Files

README.Rmd

Owner

GitHub Events

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Last Year

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Past Year

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Packages

bioconductor.org: syntenet

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Maintainers (1)

Dependencies