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circRNAprofiler

https://github.com/aufiero/circrnaprofiler

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (16.3%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene ontology immune-repertoire grna-sequence proteomics random-effects spatial-transcriptomics heatmap interactive-visualizations
Last synced: 7 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: Aufiero
  • Language: HTML
  • Default Branch: master
  • Size: 13.5 MB
Statistics
  • Stars: 10
  • Watchers: 1
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Created about 7 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



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

[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2FAufiero%2FcircRNAprofiler&count_bg=%2379C83D&title_bg=%23555555&icon=&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com) 

# circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs

circRNAprofiler is an R-based framework that only requires an R installation
and offers 15 modules for a comprehensive in silico analysis of circRNAs. 
This computational framework allows to combine and analyze circRNAs previously
detected by multiple publicly available annotation-based circRNA detection tools.
It covers different aspects of circRNAs analysis from differential expression
analysis, evolutionary conservation, biogenesis to functional analysis. The 
pipeline used by circRNAprofiler is highly automated and customizable. Furthermore,
circRNAprofiler includes additional functions for data visualization which 
facilitate the interpretation of the results.

## Installation

You can install the latest release of circRNAprofiler from Bioconductor using:
```{r, eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("circRNAprofiler")
```

To install the latest development version use:
```{r, eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("circRNAprofiler")
```

## Documentation
Detailed information on using this package can be found in the package vignettes:

```{r, eval = FALSE}
browseVignettes("circRNAprofiler")
```

## Bugs and Issues
We work hard to ensure that circRNAprofiler is a powerful tool empowering your
research. However, no software is free of bugs and issues, therefore we would 
love to get feedback from our users.

## Citation
If you find this code useful in your research, please cite:

Aufiero, S., Reckman, Y.J., Tijsen, A.J. et al. circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs. BMC Bioinformatics 21, 164 (2020). https://doi.org/10.1186/s12859-020-3500-3

Owner

  • Login: Aufiero
  • Kind: user

GitHub Events

Total
  • Push event: 4
  • Create event: 1
Last Year
  • Push event: 4
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 229
  • Total Committers: 5
  • Avg Commits per committer: 45.8
  • Development Distribution Score (DDS): 0.079
Past Year
  • Commits: 26
  • Committers: 4
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.231
Top Committers
Name Email Commits
LAPTOP-LS60IEJD\simoa s****o@g****m 211
Nitesh Turaga n****a@g****m 12
simoauf s****a@i****m 2
J Wokaty j****y@s****u 2
J Wokaty j****y 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 imunotx.com: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 15
  • Total pull requests: 0
  • Average time to close issues: 11 days
  • Average time to close pull requests: N/A
  • Total issue authors: 12
  • Total pull request authors: 0
  • Average comments per issue: 7.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • JianGuoZhou3 (3)
  • mw-neuro (2)
  • prisca399 (1)
  • EricSHo (1)
  • 1kabutar (1)
  • adenotp (1)
  • marvel479 (1)
  • Li-Yaoting (1)
  • simeix00 (1)
  • pimi17 (1)
  • xiongxxp (1)
  • ShixiangWang (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 13,063 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: circRNAprofiler

circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 13,063 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 24.6%
Downloads: 73.8%
Maintainers (1)
simo.aufiero@gmail.com
Last synced: 8 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2.0 depends
  • AnnotationHub * imports
  • BSgenome * imports
  • BSgenome.Hsapiens.UCSC.hg19 * imports
  • Biostrings * imports
  • DESeq2 * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • R.utils * imports
  • S4Vectors * imports
  • dplyr * imports
  • edgeR * imports
  • ggplot2 * imports
  • gwascat * imports
  • magrittr * imports
  • readr * imports
  • reshape2 * imports
  • rlang * imports
  • rtracklayer * imports
  • seqinr * imports
  • stats * imports
  • stringi * imports
  • stringr * imports
  • universalmotif * imports
  • utils * imports
  • BSgenome.Hsapiens.UCSC.hg38 * suggests
  • BSgenome.Mmusculus.UCSC.mm10 * suggests
  • BSgenome.Mmusculus.UCSC.mm9 * suggests
  • BiocManager * suggests
  • VennDiagram * suggests
  • devtools * suggests
  • ggpubr * suggests
  • gridExtra * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests