cRegulome
An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer
Science Score: 10.0%
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
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer
Basic Info
- Host: GitHub
- Owner: ropensci
- Language: R
- Default Branch: master
- Homepage: https://docs.ropensci.org/cRegulome
- Size: 3.07 MB
Statistics
- Stars: 3
- Watchers: 6
- Forks: 4
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
cRegulome
Overview
Transcription factors and microRNAs are important for regulating the gene expression in normal physiology and pathological conditions. Many bioinformatics tools were built to predict and identify transcription factors and microRNA targets and their role in development of diseases including cancers. The availability of public access high-throughput data allowed for data-driven predictions and discoveries. Here, we build on some of these tools and integrative analyses and provide a tool to access, manage and visualize data from open source databases. cRegulome provides a programmatic access to the regulome (microRNA and transcription factor) correlations with target genes in cancer. The package obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides classes and methods to interact with and visualize the correlation data.
What is cRegulome used for?
cRegulome provides programmatic access to regulome-gene correlation data in cancer from different data sources. Researches who are interested in studying the role of microRNAs and transcription factors in cancer can use this package to construct a small or large scale queries to answer different questions:
- Which microRNAs and/or transcription factors are associated with a particular
set of genes?
- What different regulation patterns a microRNA or a transcription factor can
take in different types of cancer?
- For a given set of regulatory elements, which genes are likely to be
regulated by these elements in a certain type of cancer?
In addition, cRegulome can be used with other R packages like igraph to
study the co-regulation networks in different types of cancer.
Getting started
To get starting with cRegulome we show a very quick example. We first start by downloading a small test database file, make a simple query and convert the output to a cRegulome object to print and visualize.
```r
install the package from CRAN
install.packages('cRegulome') ```
```r
install the development version from github
devtools::install_github('ropensci/cRegulome')
install the development version and build vignette from github
devtools::installgithub('ropensci/cRegulome', buildvignettes = TRUE) ```
```{r load_libraries}
load required libraries
library(cRegulome) library(RSQLite) library(ggplot2) ```
```r if(!file.exists('cRegulome.db')) { get_db(test = TRUE) }
connect to the db file
conn <- dbConnect(SQLite(), 'cRegulome.db') ```
Or access the same test set file from the package directly
```r
locate the testset file and connect
fl <- system.file('extdata', 'cRegulome.db', package = 'cRegulome') conn <- dbConnect(SQLite(), fl) ```
```r
enter a custom query with different arguments
dat <- getmir(conn, mir = 'hsa-let-7g', study = 'STES', minabscor = .3, maxnum = 5)
make a cmicroRNA object
ob <- cmicroRNA(dat) ```
```r
print object
ob ```
Documentation
r
browseVignettes("cRegulome")
Alternatively, the vingettes can be found online, case_study
and using_cRegulome.
Citation
r
citation("cRegulome")
Owner
- Name: rOpenSci
- Login: ropensci
- Kind: organization
- Email: info@ropensci.org
- Location: Berkeley, CA
- Website: https://ropensci.org/
- Twitter: rOpenSci
- Repositories: 307
- Profile: https://github.com/ropensci
GitHub Events
Total
- Issue comment event: 1
Last Year
- Issue comment event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| MahShaaban | m****y@s****g | 88 |
| Mahmoud Ahmed | m****d@M****l | 27 |
| Peter Hickey | p****y@g****m | 5 |
| Maëlle Salmon | m****n@y****e | 1 |
| ropenscibot | m****t@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 2 years ago
All Time
- Total issues: 4
- Total pull requests: 8
- Average time to close issues: 2 days
- Average time to close pull requests: about 9 hours
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 2.0
- Average comments per pull request: 0.13
- Merged pull requests: 8
- 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
- maelle (1)
- MahShaaban (1)
- loostchen (1)
- sckott (1)
Pull Request Authors
- PeteHaitch (4)
- MahShaaban (3)
- maelle (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
cran.r-project.org: cRegulome
Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
- Homepage: https://docs.ropensci.org/cRegulome
- Documentation: http://cran.r-project.org/web/packages/cRegulome/cRegulome.pdf
- License: GPL-3
- Status: removed
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Latest release: 0.3.2
published almost 6 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 2.10.0 depends
- DBI * imports
- R.utils * imports
- RSQLite * imports
- UpSetR * imports
- VennDiagram * imports
- ggplot2 * imports
- ggridges * imports
- graphics * imports
- grid * imports
- httr * imports
- igraph * imports
- AnnotationDbi * suggests
- clusterProfiler * suggests
- covr * suggests
- knitr * suggests
- org.Hs.eg.db * suggests
- readxl * suggests
- rmarkdown * suggests
- testthat * suggests