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ggseqlogo

Publication-quality sequence logos in R

https://github.com/omarwagih/ggseqlogo

Science Score: 36.0%

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
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Publication-quality sequence logos in R

Basic Info
  • Host: GitHub
  • Owner: omarwagih
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 10.8 MB
Statistics
  • Stars: 220
  • Watchers: 12
  • Forks: 32
  • Open Issues: 30
  • Releases: 0
Created over 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

ggseqlogo logo

ggseqlogo is an R package for generating publication-ready sequence logos using ggplot2.

Getting started

First install ggseqlogo from github using the devtools package:

r devtools::install_github("omarwagih/ggseqlogo")

Load up the package and sample data

```r

Load the required packages

require(ggplot2) require(ggseqlogo)

Some sample data

data(ggseqlogo_sample)

```

Then draw a sequence logo

```r

Plot DNA sequence logo for transcription factor - data from JASPAR

ggseqlogo( seqs_dna$MA0001.1 )

Plot protein sequence logo for kinase target phosphosites

ggseqlogo( seqs_aa$AKT1 ) ```

For more examples, and a list of features see the full tutorial here.

Tutorial

A detailed tutorial on how to use ggseqlogo can be found here.

Citation

If you use ggseqlogo, please cite:

Wagih, Omar. ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics 33, no. 22 (2017): 3645-3647. https://doi.org/10.1093/bioinformatics/btx469 PMID: 29036507

Feedback

If you have any feedback or suggestions, drop me a line at (omarwagih(at)gmail.com) or open an issue on github.

Owner

  • Name: Omar Wagih
  • Login: omarwagih
  • Kind: user
  • Location: Toronto, Canada
  • Company: Deep Genomics

GitHub Events

Total
  • Issues event: 4
  • Watch event: 14
  • Issue comment event: 2
  • Pull request event: 1
  • Fork event: 2
Last Year
  • Issues event: 4
  • Watch event: 14
  • Issue comment event: 2
  • Pull request event: 1
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 33
  • Total Committers: 1
  • Avg Commits per committer: 33.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Omar Wagih o****h@g****m 33

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 37
  • Total pull requests: 5
  • Average time to close issues: 3 months
  • Average time to close pull requests: almost 3 years
  • Total issue authors: 35
  • Total pull request authors: 5
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.2
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 1
  • Average time to close issues: 15 minutes
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • moa4020 (2)
  • ewallace (2)
  • aroelo (1)
  • rongxinzh (1)
  • dxl3742 (1)
  • kaufm202 (1)
  • durrantmm (1)
  • egenomics (1)
  • lxavierneves (1)
  • jglavina (1)
  • pwwang (1)
  • wshen2 (1)
  • MattBrauer (1)
  • Brochiert (1)
  • danli349 (1)
Pull Request Authors
  • soumitrakp (1)
  • cvaske (1)
  • AliSajid (1)
  • ewallace (1)
  • aviezerl (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 3,929 last-month
  • Total docker downloads: 22,345
  • Total dependent packages: 8
    (may contain duplicates)
  • Total dependent repositories: 27
    (may contain duplicates)
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: ggseqlogo

A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos

  • Versions: 3
  • Dependent Packages: 7
  • Dependent Repositories: 22
  • Downloads: 3,929 Last month
  • Docker Downloads: 22,345
Rankings
Stargazers count: 2.3%
Forks count: 3.0%
Dependent repos count: 5.8%
Dependent packages count: 6.6%
Average: 8.3%
Downloads: 8.9%
Docker downloads count: 23.5%
Maintainers (1)
omarwagih@gmail.com
Last synced: 10 months ago
conda-forge.org: r-ggseqlogo
  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 5
Rankings
Dependent repos count: 14.8%
Average: 26.6%
Stargazers count: 27.9%
Dependent packages count: 29.0%
Forks count: 34.7%
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • ggplot2 * imports
  • knitr * suggests
  • rmarkdown * suggests