motifStack statistics

info info

Citations per year

info

Popular tool citations

chevron_left Sequence logo generation chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

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

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Jianhong Ou

motifStack citations

 (9)
library_books

Detection of hyper conserved regions in hepatitis B virus X gene potentially useful for gene therapy

2018
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), […]

library_books

Analysis of hepatitis B virus preS1 variability and prevalence of the rs2296651 polymorphism in a Spanish population

2018
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 […]

library_books

Abundant expression of somatic transposon derived piRNAs throughout Tribolium castaneum embryogenesis

2017
Genome Biol
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 […]

library_books

Transcription factor Hlx controls a systematic switch from white to brown fat through Prdm16 mediated co activation

2017
Nat Commun
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 […]

library_books

Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants

2016
BMC Genomics
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 […]

library_books

TSS EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens

2016
BMC Genomics
PMCID: 5094136
PMID: 27806702
DOI: 10.1186/s12864-016-3211-3

[…] transtermhp v2.09 []. the program is run with standard parameter values, and an annotation file containing coordinates of all annotated genes., all sequence logos were generated with the r package motifstack from bioconductor, and using the background correction to adjust the signal according to gc content of the organism []., additional file 1: table s1. additional file 2: figure s1. […]


Want to access the full list of citations?

motifStack reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review motifStack