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motifStack specifications

Information


Unique identifier OMICS_19821
Name motifStack
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.24.1
Stability Stable
Requirements
methods, stats, RColorBrewer, grid, graphics, BiocGenerics, utils, Biostrings, BiocStyle, stats4, grDevices, RUnit, scales, knitr, ade4, R(>=2.15.1), htmlwidgets, XML, MotifDb, grImport, MotIV
Maintained Yes

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Maintainer


  • person_outline Jianhong Ou <>

motifStack in publications

 (9)
PMCID: 5960815
DOI: 10.3748/wjg.v24.i19.2095

[…] 1 (nt or aa). for each window, the analysis computes the mean ic of each position within the window. in addition, the results are represented as sequence logos created using the r language package motifstack[]., the bioinformatics methods used in this study were reviewed by dr. josep gregori from the liver disease-viral hepatitis laboratory of vall d’hebron hospital (barcelona, spain), […]

PMCID: 5807671
PMID: 29456407
DOI: 10.3748/wjg.v24.i6.680

[…] = log2 (20)- 4.322 = 0. these calculations in the regions of ntcp interaction (47 aa) and virion morphogenesis (22 aa) were also represented as sequence logos created using the r language package, motifstack[]., the statistical and bioinformatics methods used in this study were reviewed by dr. josep gregori from the liver disease-viral hepatitis laboratory (vall d’hebron institut […]

PMCID: 5613491
PMID: 28950880
DOI: 10.1186/s13059-017-1304-1

[…] reads were split equally between the possible targets., nucleotide frequencies of pirna reads at each position were calculated using a custom script, and sequence logos were plotted using the “motifstack” r package., ping-pong signatures were calculated following the procedure described in []. in brief, we extracted 25–35-nt sense–antisense read pairs and calculated the number […]

PMCID: 5507986
PMID: 28701693
DOI: 10.1038/s41467-017-00098-2

[…] algorithm) was downloaded from uniprobe database (http://thebrain.bwh.harvard.edu/uniprobe), . the motif was trimmed by information content no less than 0.4 in both ends by r/bioconductor package motifstack (version 1.14.0). published prdm16 peaks of brown adipocytes were downloaded and annotated by r/bioconductor package chippeakanno (version 3.5.1). the sequences of the prdm16 peaks […]

PMCID: 5093975
PMID: 27806710
DOI: 10.1186/s12864-016-3202-4

[…] jordan being amongst the most highly expressed repeat elements in the sample., all sequence logos were based on the adapter- and quality score-trimmed reads, and were generated using the r package motifstack (ou and zhu, r package version 1.12.0)., all sequences of mirnas of v. carteri and c. reinhardtii (mirbase) were subjected to a multiple sequence alignment using clustalw []. the resulting […]


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