ArticlePloS one2022
ggmotif: An R Package for the extraction and visualization of motifs from MEME software.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 12 citations in OpenAlex.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MEME (Multiple Em for Motif Elicitation) is the most commonly used tool to identify motifs within deoxyribonucleic acid (DNA) or protein sequences. However, the results generated by the MEMEare saved using file formats .xml and .txt, which are difficult to read, visualize, or integrate with other widely used phylogenetic tree packages, such as ggtree. To overcome this problem, we developed the ggmotif R package, which provides two easy-to-use functions that can facilitate the extraction and visualization of motifs from the results files generated by the MEME. ggmotif can extract the information of the location of motif(s) on the corresponding sequence(s) from the .xml format file and visualize it. Additionally, the data extracted by ggmotif can be easily integrated with the phylogenetic data. On the other hand, ggmotif can obtain the sequence of each motif from the .txt format file and draw the sequence logo with the function ggseqlogo from the ggseqlogo R package. The ggmotif R package is freely available (including examples and vignettes) from GitHub at https://github.com/lixiang117423/ggmotif or from CRAN at https://CRAN.R-project.org/package=ggmotif.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.