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CircSeqAlignTk

An R package for end-to-end analysis of RNA-seq data for circular genome

https://github.com/bitdessin/CircSeqAlignTk

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 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene
Last synced: 6 months ago · JSON representation

Repository

An R package for end-to-end analysis of RNA-seq data for circular genome

Basic Info
  • Host: GitHub
  • Owner: bitdessin
  • License: mit
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 1.61 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 3 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

CircSeqAlignTk

End-to-End Analysis of Small RNA-Seq Data from Viroids

CircSeqAlignTk is an end-to-end toolkit for RNA-Seq data analysis of circular genome sequences, supporting tasks from alignment to visualization. It is primarily designed for studying viroids, which are small, circular RNAs typically composed of a few hundred nucleotides. In addition to analysis capabilities, CircSeqAlignTk provides a streamlined interface for generating synthetic RNA-Seq data that closely mimics real datasets. This functionality enables developers to benchmark alignment tools, test novel alignment algorithms, and validate new workflows.

Installation

To install the CircSeqAlignTk package, start R (≥ 4.2) and run the following steps:

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

BiocManager::install('CircSeqAlignTk') ```

Note that to install the latest version of the CircSeqAlignTk package, the latest version of R is required.

Documentation

Vignette, including overview of CircSeqAlignTk package, detailed explanation of functions, and several case studies, can be accessed with the following code.

browseVignettes('CircSeqAlignTk')

Citation

Sun J, Fu X and Cao W. CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes. F1000Research 2024, 11:1221. doi: 10.12688/f1000research.127348.2.

Owner

  • Name: bitdessin
  • Login: bitdessin
  • Kind: organization

GitHub Events

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

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 25
  • Total Committers: 4
  • Avg Commits per committer: 6.25
  • Development Distribution Score (DDS): 0.6
Past Year
  • Commits: 8
  • Committers: 4
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.625
Top Committers
Name Email Commits
J Wokaty j****y@s****u 10
jsun s****n@a****p 9
jsun s****n@b****v 4
A Wokaty a****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2 biunit.dev: 1 aabbdd.jp: 1

Issues and Pull Requests

Last synced: 7 months ago

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  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
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  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
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Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • BiocGenerics * imports
  • Biostrings * imports
  • IRanges * imports
  • Rbowtie2 * imports
  • Rhisat2 * imports
  • Rsamtools * imports
  • S4Vectors * imports
  • ShortRead * imports
  • dplyr * imports
  • ggplot2 * imports
  • magrittr * imports
  • methods * imports
  • rlang * imports
  • stats * imports
  • tidyr * imports
  • tools * imports
  • utils * imports
  • BiocStyle * suggests
  • R.utils * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests