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DiffLogo specifications

Information


Unique identifier OMICS_10707
Name DiffLogo
Alternative name WebDiffLogo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA/RNA/protein sequences, matrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.4.0
Stability Stable
Requirements
stats, graphics, utils, testthat, grDevices, tools, seqLogo, knitr, R(>=3.4), cba, MotifDb
Maintained Yes

Versioning


Add your version

Documentation


Maintainers


  • person_outline Hendrik Treutler <>
  • person_outline Ivo Grosse <>

Additional information


A web app of DiffLogo (called WebDiffLogo) is available to http://difflogo.com/

Information


Unique identifier OMICS_10707
Name DiffLogo
Alternative name WebDiffLogo
Interface Web user interface
Restrictions to use None
Input data Motif files from four cell lines.
Input format TXT, FASTA, HOMER, JASPAR, PFM, PWM
Programming languages Javascript, R
License GNU Lesser General Public License version 2.1
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Hendrik Treutler <>
  • person_outline Ivo Grosse <>

Additional information


A web app of DiffLogo (called WebDiffLogo) is available to http://difflogo.com/

Publication for DiffLogo

DiffLogo in publications

 (5)
PMCID: 5915569
PMID: 29720995
DOI: 10.3389/fpls.2018.00519

[…] difference can be visualized by comparing the frequencies of these position-specific bases in m5c and non- m5c modifications (figure ). furthermore, through two sample logo analysis using r package “difflogo” (nettling et al., ), we discovered the similar trend of some specific nucleotide usage preferences around m5c modifications (figure ). these results indicate that base frequency differences […]

PMCID: 5663106
PMID: 29084609
DOI: 10.1186/s13059-017-1332-x

[…] the 5′ utr (fig. ). to perceive differences between the motifs identified by meme, we performed a clustering analysis based on pairwise comparison between motifs across regions using the r package difflogo (additional file : figure s6a). in the resulting distance tree, the exon and 5′ utr motifs clustered together and consequently were closely related. in contrast, the 3′ utr motif is located […]

PMCID: 5731801
PMID: 28783426
DOI: 10.1080/15476286.2017.1349048

[…] to the sense strand or antisense strand, and non-“ping-pong” reads mapping to the sense strand or antisense strand of either transposable elements or genes. the resulting matrices were plotted using difflogo., pirna cluster detection was performed on nematostella pirnas using the protrac pipeline version 2.1 with the options protrac_nv (supplemental table s3) for each developmental stage. […]

PMCID: 5512977
PMID: 28637323
DOI: 10.1093/gbe/evx108

[…] contained all repeats showing an rvd swap within annotale classes at this position. we analyzed the flanking sequences of repeats not involved in rvd swaps for each repeat type and generated a difflogo () for each pair of repeat types to check whether the flanking sequences show differences depending on the repeat type., we additionally calculated the mutual information of each flanking […]

PMCID: 4862171
PMID: 27165633
DOI: 10.1186/s12864-016-2682-6

[…] than 21 bp, which is the length of the longest motif (nrsf) in the performed studies. table shows details about the resulting data. all data are available as additional file ., we used the r package difflogo [] to depict the differences between the predicted motifs of the models \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepac […]


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DiffLogo institution(s)
Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
DiffLogo funding source(s)
This work was supported by DFG (grant no. GR3526/1).

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