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About the developer

omarwagih
141 Stars 20 Forks 33 Commits 7 Opened issues

Description

Publication-quality sequence logos in R

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

Load up the package and sample data

# Load the required packages
require(ggplot2)
require(ggseqlogo)

Some sample data

data(ggseqlogo_sample)

Then draw a sequence logo

# 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.

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