polymapR protocols

View polymapR computational protocol

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polymapR specifications

Information


Unique identifier OMICS_24785
Name polymapR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data A phased integrated map.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.17
Stability Stable
Requirements
RColorBrewer, rmarkdown, knitr, reshape2, foreach, Hmisc, R(≥3.2.0), igraph, combinat, doParallel, MDSMap, LPmerge
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Roeland E. Voorrips <>
  • person_outline Peter Bourke <>
  • person_outline Chris Maliepaard <>

Publication for polymapR

polymapR in pipeline

2009
PMCID: 2762536
PMID: 19434427
DOI: 10.1007/s00439-009-0677-y

[…] potential regulatory snps. mapper is a companion tool to the snpper retrieval system and database that locates computationally predicted transcription factor-binding sites (riva and kohane ). both polymapr (freimuth et al. ) and pupasnp finder (conde et al. ) use computational methods to find possible exon splicing enhancer sites that can then be mapped to snp locations to find snps […]


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polymapR in publication

PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] however, tetraploidy is the most common polyploid condition () and therefore this software is still relevant for a broad range of species., recently, an alternative linkage mapping package called polymapr was released, which is described in a pre-print manuscript (bourke et al., unpublished). like tsnpm, polymapr used dosage-scored marker information from f1 populations to estimate […]


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polymapR institution(s)
Plant Breeding, Wageningen University & Research, PB Wageningen, The Netherlands; Horticulture and Product Physiology, Wageningen University & Research, PB Wageningen, The Netherlands; Biometris, Wageningen University & Research, PB Wageningen, The Netherlands; Van Zanten Breeding B. V., EW, Rijsenhout, The Netherlands
polymapR funding source(s)
Supported through the TKI projects “A genetic analysis pipeline for polyploid crops” (project number BO-26.03-002- 001) and “Novel genetic and genomic tools for polyploid crops” (project number BO-26.03- 009-004).

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