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Citations per year

Number of citations per year for the bioinformatics software tool motifStack
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Tool usage distribution map

This map represents all the scientific publications referring to motifStack per scientific context
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Associated diseases

This word cloud represents motifStack usage per disease context
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Protocols

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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Documentation


Maintainer


  • person_outline Jianhong Ou

motifStack citations

 (11)
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

[…] 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 […]

library_books

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

2018
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 […]

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

[…] 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 […]

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

[…] 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 […]

call_split

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
call_split See protocol

[…] ble 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 were use […]

library_books

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

2016
F1000Res
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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