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Dagr specifications

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Unique identifier OMICS_25661
Name Dagr
Alternative name Directed Acyclic GRaphs
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Scala
License MIT License
Computer skills Advanced
Version 0.2.0
Stability Stable
Maintained Yes

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  • person_outline Tim Fennell <>

Dagr in pipelines

 (6)
2018
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] ensembl ids were used as input and bonferroni correction for multiple testing (p-value <0.05) was used while determining the fold enrichment. to understand the relationship between go terms, directed acyclic graphs of significantly enriched go terms were drawn using goview (webgestalt.org/goview)., to determine the overlap between dmrs and gene expression, we compared the gene annotation […]

2014
PMCID: 3995336
PMID: 24497029
DOI: 10.1093/molbev/msu062

[…] background distribution, which was independently contrasted with distributions of functions within strongly separated and strongly conserved sets of trs. the complete enrichment data set including directed acyclic graphs of enriched go terms is available at http://www.atgc-montpellier.fr/tre (last accessed february 20, 2014)., for all pairwise alignments of human–mouse tr-containing orthologs […]

2013
PMCID: 3669298
PMID: 23741328
DOI: 10.1371/journal.pone.0064410

[…] contig sequences were then annotated according to the following parameters: a pre-e-value-hit-filter of 10−6, a pro-similarity-hit-filter of 15, an annotation cut-off of 55, and a go weight of 5. directed acyclic graphs (dag’s) were generated using a sequence filter of 5, an alpha score of 0.6 and a 0 node score filter. a score was computed at each node by blast2go to highlight areas of high […]

2012
PMCID: 3400982
PMID: 22829738
DOI: 10.6026/97320630008595

[…] hidden markov model (hmm) pfam database []. the go-terms were obtained using gene ontology database that cross linked at uniprot database. we used go hierarchies of arabidosis thaliana to obtain go directed acyclic graphs (dag). this graph was explained using cytoscape 2.8.1 version []., we proposed an algorithm to obtain functional distances using sum of distance values between go terms […]

2012
PMCID: 3507654
PMID: 22704053
DOI: 10.1186/1755-8794-5-25

[…] entrez ids for predicted targets that were known to be differentially expressed based on our previous study [] was uploaded to the web application webgestalt gene set analysis toolkit version 2 []. directed acyclic graphs (dags) were generated representing a hierarchical categorization of the significant go annotations., potential target gene interactions were analyzed via networks generated […]

Dagr in publications

 (423)
PMCID: 5917267
PMID: 29725313
DOI: 10.3389/fpsyg.2018.00547

[…] has been a strong interest in representing multivariate data as networks. one of these networks, the markov network, is based on undirected acyclic graphs (friedman, ), whereas directed graphs (directed acyclic graphs, i.e., dags) are bayesian networks. graph networks come from the process of high-dimensional data and provide a framework for modeling how several variables are mutually […]

PMCID: 5908917
PMID: 29674673
DOI: 10.1038/s41598-018-24645-z

[…] go annotation is a process of scoring the similarity between the target sequence and the sequence to be aligned to determine the reliability of the source of the go term and the go term structure in directed acyclic graphs. only the go term that satisfies the preset score may be annotated to the target protein sequence. for the supplementary annotation augmentation, the conservative motif […]

PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] ensembl ids were used as input and bonferroni correction for multiple testing (p-value <0.05) was used while determining the fold enrichment. to understand the relationship between go terms, directed acyclic graphs of significantly enriched go terms were drawn using goview (webgestalt.org/goview)., to determine the overlap between dmrs and gene expression, we compared the gene annotation […]

PMCID: 5887019
PMID: 29623440
DOI: 10.1186/s13321-018-0273-z

[…] planning concepts. in the “” section, we point out problems that can arise when using unary-binary trees for modeling synthesis plans, and demonstrate how to solve these problems by the use of directed acyclic graphs and hypergraphs. we define a structure called a hypergraph of reactions, which we prove contains all synthesis plans as hyperpaths (theorem ). we then show how this allows us […]

PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] other approaches offer trainable networks that can learn chemical feature representations that are optimized for a particular prediction task. lusci et al. [] applied recursive neural networks for directed acyclic graphs to undirected molecular graphs by creating an ensemble of directed graphs in which one atom is selected as the root node. graph convolutions on undirected molecular graphs […]

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