TreeMap pipeline

TreeMap specifications

Information


Unique identifier OMICS_08814
Name TreeMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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TreeMap IN pipelines

 (3)
2017
PMCID: 5591248
PMID: 28887440
DOI: 10.1038/s41598-017-10059-w

[…] were generated using the paver 2.0 software (decodon gmbh, greifswald, germany). the application uses functional annotations on several levels and displays them in one interactive voronoi-like treemap image. the functional annotation data was extracted from the latest “theseed.org” build58, 59 (extraction date: 9th of december 2015) for s. aureus nctc8325 and s. aureus col. the template […]

2017
PMCID: 5591248
PMID: 28887440
DOI: 10.1038/s41598-017-10059-w

[…] treemap image. the functional annotation data was extracted from the latest “theseed.org” build58, 59 (extraction date: 9th of december 2015) for s. aureus nctc8325 and s. aureus col. the template treemap calculation of each strain was performed using the free swarm algorithm. the length of each protein (amino acid count) was normalized to the amino acid count of the largest protein […]

2016
PMCID: 5111228
PMID: 27846799
DOI: 10.1186/s12864-016-3251-8

[…] using the goseq package in bioconductor 3.0 [100] and go trimming [101]. revigo was used to reduce redundancy and produce treemaps (space-filling visualization of hierarchical structures) using the treemap package in r [54]. default parameters were used and the redundancy threshold (allowed similarity) was set at 0.4 (very small)., sequences of mapk, pka and rim proteins from s. cerevisiae […]

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