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motifStack specifications


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
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




No version available



  • person_outline Jianhong Ou

motifStack citations


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

PMCID: 5960815
DOI: 10.3748/wjg.v24.i19.2095

[…] of 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), CIBERehd r […]


ATACseqQC: a Bioconductor package for post alignment quality assessment of ATAC seq data

BMC Genomics
PMCID: 5831847
PMID: 29490630
DOI: 10.1186/s12864-018-4559-3

[…] ome package [, ] to search potential binding sites for a given DNA-binding protein, represent the matched genomic coordinates as GenomicRanges objects, and plot the motif as a sequence logo using the motifStack package []. The factorFootprints function first uses the matchPWM function to predict the binding sites with an input position weight matrix (PWM) for a DNA-binding protein. Next, it calcul […]


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

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

[…] aa = 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 Recerca-Hospital […]


Abundant expression of somatic transposon derived piRNAs throughout Tribolium castaneum embryogenesis

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

[…] strand, 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 of overlapping […]


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

Nat Commun
PMCID: 5507986
PMID: 28701693
DOI: 10.1038/s41467-017-00098-2
call_split See protocol

[…] ble algorithm) was downloaded from UniProbe database (, . 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 were use […]


TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] cs grDevices utils 15 [8] datasets methods base 16 17 other attached packages : 18 [1] rGADEM _ 2.20.0 19 [2] seqLogo _ 1.38.0 20 [3] BSgenome _ 1.40.1 21 [4] rtracklayer _ 1.32.1 22 [5] motifStack _ 1.16.2 23 [6] ade4 _ 1.7–4 24 [7] grImport _ 0.9–0 25 [8] XML _ 3.98–1.4 26 [9] MotIV _ 1.28.0 27 [10] pathview _ 1.12.0 28 [11] biomaRt _ 2.28.0 29 [12] minet _ 3.30.0 30 [13 […]


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