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ceRNAnetsim

Simulation of interactions miRNA:Competing Targets

https://github.com/selcenari/cernanetsim

Science Score: 46.0%

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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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
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    Academic publication links
    Links to: ncbi.nlm.nih.gov, nature.com
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary

Keywords

cerna mirna network-biology network-simulator r tcga tidygraph tidyverse

Keywords from Contributors

bioconductor-package gene grna-sequence genomics ontology immune-repertoire sequencing proteomics
Last synced: 6 months ago · JSON representation

Repository

Simulation of interactions miRNA:Competing Targets

Basic Info
  • Host: GitHub
  • Owner: selcenari
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 28.9 MB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Topics
cerna mirna network-biology network-simulator r tcga tidygraph tidyverse
Created almost 7 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog

README.md

ceRNAnetsim

License: GPL v3 Binder Travis build status Codecov test coverage <!-- badges: end -->

ceRNAnetsim helps to understanding complex miRNA:target interactions with the network based approach. It utilizes the amounts of miRNAs and their targets and interaction parameters optionally.

Installation

Installation of ceRNAnetsim:

```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("ceRNAnetsim")

library(ceRNAnetsim)

```

Example

``` data("minsamp")

minsamp

priminggraph(minsamp, competingcount = Competingexpression, miRNAcount = miRNA_expression)

```

Local Files

The ceRNAnetsim provides various datasets for experimenting with package functions. These are:

  • minsamp : the minimum sample consists of 2 miRNAs and 6 genes which are targeted by them. new_counts is a helper dataset for minsamp.
  • midsamp : middle-sized sample is a network of 4 miRNAs and 20 competing target genes.
  • huge_example : this dataset is comprised of a large network which incorporates three datasets:
    • gene expression levels (RNA-Seq) retrieved from TCGA-BRCA breast cancer
    • miRNA expression of a breast cancer patient (from TCGA)
    • and the miRNA:target dataset gathered from two different high-throughput experimental studies. (CLASH & CLEAR-CLiP methods)
  • The remaining datasets are used as reproducible example of methods shown as Mirtarbase example

Vignettes

The repository of ceRNAnetsim contents the vignettes that follow:

Also see package webpage

Issues

Contact us for any issue or bug via:

Owner

  • Login: selcenari
  • Kind: user
  • Location: Istanbul
  • Company: Yildiz Technical University

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 427
  • Total Committers: 4
  • Avg Commits per committer: 106.75
  • Development Distribution Score (DDS): 0.126
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Selcen Ari s****i@g****m 373
Alper Yilmaz a****z@g****m 38
Nitesh Turaga n****a@g****m 10
J Wokaty j****y@s****u 6
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 10
  • Average time to close issues: N/A
  • Average time to close pull requests: 28 minutes
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 9
  • 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
Pull Request Authors
  • selcenari (13)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 8,050 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: ceRNAnetsim

Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,050 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 26.1%
Downloads: 78.3%
Maintainers (1)
selcenarii@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • dplyr * depends
  • tidygraph * depends
  • furrr * imports
  • future * imports
  • ggplot2 * imports
  • ggraph * imports
  • igraph * imports
  • purrr * imports
  • rlang * imports
  • stats * imports
  • tibble * imports
  • tidyr * imports
  • covr * suggests
  • knitr * suggests
  • png * suggests
  • rmarkdown * suggests
  • testthat * suggests