Science Score: 23.0%
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
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.1%) to scientific vocabulary
Keywords from Contributors
genomics
bioconductor-package
Last synced: 11 months ago
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JSON representation
Repository
Finding an Active Metabolic Module in Atom Transition Network
Basic Info
- Host: GitHub
- Owner: ctlab
- License: other
- Language: R
- Default Branch: master
- Size: 3.74 MB
Statistics
- Stars: 7
- Watchers: 12
- Forks: 4
- Open Issues: 1
- Releases: 0
Created over 9 years ago
· Last pushed about 2 years ago
Metadata Files
Readme
README.Rmd
---
output: github_document
---
[](https://github.com/ctlab/gatom/actions/workflows/R-CMD-check.yaml)
# gatom
An R-package for finding active metabolic modules in atom transition network.
Full vignette can be found [here](https://rpubs.com/asergushichev/gatom-tutorial).
### Installation
```{r eval=FALSE}
library(devtools)
install_github("ctlab/gatom")
```
### Quick start
```{r message=FALSE}
library(gatom)
library(data.table)
library(igraph)
library(mwcsr)
```
First let's load data with atom mappings (`network` object),
enzyme annotations for mouse (`org.Mm.eg.gatom`)
and metabolite annotations (`met.kegg.db.rda`):
```{r}
data("networkEx")
data("org.Mm.eg.gatom.annoEx")
data("met.kegg.dbEx")
```
Loading input data:
```{r message=F}
data("met.de.rawEx")
data("gene.de.rawEx")
```
Getting atom graph:
```{r}
g <- makeMetabolicGraph(network=networkEx,
topology = "atoms",
org.gatom.anno=org.Mm.eg.gatom.annoEx,
gene.de=gene.de.rawEx,
met.db=met.kegg.dbEx,
met.de=met.de.rawEx)
print(g)
```
Scoring graph, obtaining an instance of SGMWCS (Signal Generalized Maximum Weight Subgraph)
problem instance:
```{r message=FALSE, warning=FALSE}
gs <- scoreGraph(g, k.gene=25, k.met=25)
```
Initialize an SMGWCS solver (a heuristic relax-and-cut solver `rnc_solver` is used for simplicity, check out `mwcsr` package documentation for more options):
```{r}
solver <- rnc_solver()
```
Finding a module:
```{r message=FALSE, warning=FALSE}
res <- solve_mwcsp(solver, gs)
m <- res$graph
```
```{r}
print(m)
head(E(m)$label)
head(V(m)$label)
```
We can save the module to different formats (dot, xgmml, svg, pdf):
```{r results="hide", message=FALSE, warning=FALSE}
saveModuleToPdf(m, file="M0.vs.M1.pdf", name="M0.vs.M1", n_iter=100, force=1e-5)
```
Owner
- Name: Computer Technologies Laboratory
- Login: ctlab
- Kind: organization
- Repositories: 70
- Profile: https://github.com/ctlab
GitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Alexey Sergushichev | a****x@g****m | 107 |
| Octopus | a****a@g****m | 28 |
| Mariia Emelianova | m****m@g****m | 11 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y@u****m | 2 |
| Alexey Sergushichev | a****g@i****u | 1 |
| Masha | n****t@m****u | 1 |
| Octopus | o****s@o****M | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 7
- Total pull requests: 9
- Average time to close issues: over 1 year
- Average time to close pull requests: 7 days
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 0.86
- Average comments per pull request: 0.44
- Merged pull requests: 6
- 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
Top Authors
Issue Authors
- assaron (5)
- gandrianov (1)
- anamariaelek (1)
Pull Request Authors
- anastasiiaNG (6)
- assaron (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 4,840 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
bioconductor.org: gatom
Finding an Active Metabolic Module in Atom Transition Network
- Homepage: https://github.com/ctlab/gatom/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/gatom/inst/doc/gatom.pdf
- License: MIT + file LICENCE
-
Latest release: 1.6.0
published about 1 year ago
Rankings
Dependent repos count: 0.0%
Forks count: 12.4%
Stargazers count: 19.6%
Dependent packages count: 31.7%
Average: 32.5%
Downloads: 98.8%
Maintainers (1)
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.5.0 depends
- BioNet * imports
- GGally * imports
- XML * imports
- data.table * imports
- ggplot2 * imports
- grid * imports
- igraph * imports
- intergraph * imports
- methods * imports
- mwcsr * imports
- network * imports
- plyr * imports
- pryr * imports
- sna * imports
- AnnotationDbi * suggests
- BiocStyle * suggests
- KEGGREST * suggests
- R.utils * suggests
- fgsea * suggests
- knitr * suggests
- org.Mm.eg.db * suggests
- reactome.db * suggests
- readr * suggests
- rmarkdown * suggests
- testthat * suggests
.github/workflows/R-CMD-check.yaml
actions
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite