Metacoder statistics

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Metacoder specifications

Information


Unique identifier OMICS_15999
Name Metacoder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format CSV
Output format PNG, JPG, JPEG
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Niklaus Grunwald <>

Publication for Metacoder

Metacoder in pipeline

2018
PMCID: 5940145
PMID: 29535148
DOI: 10.1534/g3.118.200174

[…] interpro ids from interproscan were merged to the annotation to improve accuracy. graphical representation of go categories belonging to the 675 core-genes was obtained using the r package metacoder (). the blast2go output files were searched for the terms “sex determination” (go accession number 0007530), “sex differentiation” (0007548), “male sex differentiation” (0046661), “female […]


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Metacoder in publications

 (2)
PMCID: 5940145
PMID: 29535148
DOI: 10.1534/g3.118.200174

[…] interpro ids from interproscan were merged to the annotation to improve accuracy. graphical representation of go categories belonging to the 675 core-genes was obtained using the r package metacoder (). the blast2go output files were searched for the terms “sex determination” (go accession number 0007530), “sex differentiation” (0007548), “male sex differentiation” (0046661), “female […]

PMCID: 5704230
PMID: 29125533
DOI: 10.3390/genes8110317

[…] to transcripts based on blastx hits to the swissprot database, and enrichment analysis was performed using the bioconductor package goseq []. go term enrichment was visualized using the r package metacoder []. go term ids were converted to go terms using wego []., microsatellite simple sequence repeats (ssrs) were identified in assembled transcripts using the microsatellite identification […]


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Metacoder funding source(s)
This work was supported in part by funds from USDA ARS CRIS Project 2027-22000-039-00 and the USDA ARS Floriculture Nursery Research Initiative 2072-22000-039-15-S and National Sciences Foundation Award 1557192.

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