Graphviz protocols

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Graphviz specifications


Unique identifier OMICS_04785
Name Graphviz
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes


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Graphviz in pipelines

PMCID: 4823825
PMID: 27048880
DOI: 10.1038/ncomms11185

[…] of deletion ref′=ref+alt, alt′=alt; in case of a gene on chromosome x ref′=ref × 2+alt, alt′=alt; in case of copy neutral loh ref′=ref+alt/2 and alt′=alt/2. the reconstructed trees were redrawn in graphviz by using in-house scripts adapted from ancestree to show the trajectories of mutations with contribution ⩾0.05., we aligned rnaseq data from dipg3-pons 1 and dipg3-pons 2 (rna extraction […]

PMCID: 4102619
PMID: 24608988
DOI: 10.1038/jid.2014.127

[…] above 0.01 in at least one sample. unsupervised clustering was performed using cluster 3.0 () and visualized using treeview ()., the taxmap bubble diagrams were created by imsa, visualized using graphviz (). taxmaps show the score at each taxonomic level, in this case for the unique reads only. an average taxmap was created for normal and ssc samples by considering only the nodes present […]

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Graphviz in publications

PMCID: 5933701
PMID: 29723213
DOI: 10.1371/journal.pone.0195271

[…] the html is supplemented by the bootstrap framework ( for standard components, while d3.js [] is used to modify the visualized graphs, which are created as svg files using graphviz []. scripting is handled by javascript, often accompanied by the jquery library ( we use pubmed’s interface ( to retrieve information […]

PMCID: 5873459
PMID: 29562182
DOI: 10.1016/j.celrep.2018.02.085

[…] the graphical output of gorilla (), with directed graphs and using color coding to indicate the significance of the enrichment, the intensity of red indicating significance. graphs were drawn using graphviz., the evolutionary age of human proteins was based on the proteinhistorian database (), using the princeton protein orthology (ppod)/pantherv7 dataset, generated with asymmetric wagner […]

PMCID: 5890187
PMID: 29662487
DOI: 10.3389/fimmu.2018.00491

[…] sequences from a dominant clone together with the germline sequence were aligned using clustalw software. the output alignment was used as input in igtree©. the output tree file is visualized by graphviz 2.38. the root of the tree is the putative germline sequence and the clonally related ighv sequences are assigned to either leaves or internal nodes of the tree. each tree node represents […]

PMCID: 5824948
PMID: 29476134
DOI: 10.1038/s41598-018-22031-3

[…] logic rules-based node updates, network modification via node and edge knock-down, cell fate determination using user-defined logic and network visualization using matlab biograph object and graphviz (fig. ). the analysis pipeline includes both deterministic as well as probabilistic analyses of user-defined networks (fig. ). attractors can be visualized in the form of attractor […]

PMCID: 5731347
PMID: 29175850
DOI: 10.15252/msb.20177651

[…] natural language (fig a left, full text shown in ) and used trips to convert the description into indra statements. a node‐edge graph was generated using indra's graph assembler and rendered using graphviz (fig a, right). although different stylistically, the pathway map assembled using indra matches the original one drawn by hand in the following ways: it (i) includes the same set […]

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