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Protocols

ggseqlogo specifications

Information


Unique identifier OMICS_19820
Name ggseqlogo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A sequence alignment as a character vector or position frequency matrix.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0, GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 0.1
Stability Stable
Requirements
ggplot2, rmarkdown, knitr
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Omar Wagih

Additional information


https://omarwagih.github.io/ggseqlogo/

Publication for ggseqlogo

ggseqlogo citations

 (6)
call_split

Degenerate Pax2 and Senseless binding motifs improve detection of low affinity sites required for enhancer specificity

2018
PLoS Genet
PMCID: 5902045
PMID: 29617378
DOI: 10.1371/journal.pgen.1007289
call_split See protocol

[…] Nitta et al. [] (). PCMs were converted to PWMs using a custom R script using a pseudo-count of n (where n is the number of observed nucleotides at a position). Sequence logos were created using the ggSeqLogo package for R [].To generate PWMs in , B1H hits were (1) assigned an affinity score (defined below), (2) placed into quartiles, (3) 50 B1H hits were sampled from each quartile and (4) MEME w […]

library_books

The Ancient Link between G Protein Coupled Receptors and C Terminal Phospholipid Kinase Domains

2018
MBio
PMCID: 5784254
PMID: 29362235
DOI: 10.1128/mBio.02119-17

[…] -PIPKs was calculated in Jalview using the AMAS method (), and those data are presented as a sliding moving average calculated over 50 positions. The WebLogo for the LRxGI motif was plotted using the ggseqlogo package () in R v3.3.2. […]

library_books

Functional role of the type 1 pilus rod structure in mediating host pathogen interactions

2018
eLife
PMCID: 5798934
PMID: 29345620
DOI: 10.7554/eLife.31662.031

[…] erations of the FFT-NS-i algorithm based on the PAM200 scoring matrix (). Conservation at each amino acid position was calculated using custom Python scripts and a sequence logo was created using the ggseqlogo package in R () using RStudio ().To estimate selection pressures on each codon in fimA, we obtained all available gene sequences encoding the protein sequences described above from the Ensem […]

library_books

Mapping mutational effects along the evolutionary landscape of HIV envelope

2018
eLife
PMCID: 5910023
PMID: 29590010
DOI: 10.7554/eLife.34420.047

[…] such as read depth, per-codon mutation frequency, mutation types, etc. also contains text files and CSV files with the numerical values shown in these plots.Citations are also owed to weblogo () and ggseqlogo (), which were used in the generation of the logoplots. […]

library_books

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy

2017
Nature
PMCID: 5608080
PMID: 28854171
DOI: 10.1038/nature23666

[…] nces was generated, and read counts corresponding to sequences with up to three mismatches were combined into the most abundant sequence. Barcode sequence logograms were generated using the R package ggseqlogo (https://github.com/omarwagih/ggseqlogo). Spiked-in controls were retrieved for defining noise thresholds and clone size estimation as described previously,. We defined fractional read value […]

library_books

Cross recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high density peptide microarray epitope mapping

2017
PLoS Negl Trop Dis
PMCID: 5529020
PMID: 28708892
DOI: 10.1371/journal.pntd.0005768

[…] .1 algorithm to identify residues associated with high or low sum of scores []. Like above, the significance threshold was set to α = 0.05. The results were illustrated as sequence logos using the R “ggseqlogo” package []. […]

Citations

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ggseqlogo institution(s)
European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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