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Metacoder specifications


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




No version available



  • person_outline Niklaus Grunwald

Publication for Metacoder

Metacoder citations


Identification of General Patterns of Sex Biased Expression in Daphnia, a Genus with Environmental Sex Determination

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

[…] itionally, 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 go […]


Taxa: An R package implementing data standards and methods for taxonomic data

PMCID: 5887078
PMID: 29707201
DOI: 10.5256/f1000research.15231.r31494

[…] or the commonplace problems of data parsing and manipulation will free developers to focus on specific novel functionality. The taxa package already serves as the foundation of another package called metacoder, which provides functions for plotting taxonomic information and parsing common file formats used in metagenomics research. Taxize, the primary package for querying taxonomic information fro […]


Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome

PMCID: 5704230
PMID: 29125533
DOI: 10.3390/genes8110317

[…] ned 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 tool ( […]


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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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