(inactive) Gimpute

[Junfang]

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• Repository: https://github.com/transbioZI/Gimpute

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[bioc-issue-bot]

Hi @Junfang

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: Gimpute
Type: Package
Title: Gimpute: An efficient genetic data processing and imputation pipeline
Version: 0.99.6
Date: 2018-06-27 
Authors@R: c(person("Junfang", "Chen", role=c("aut", "cre", "cph"), email="junfang.che33@gmail.com"),
    person("Dietmar", "Lippold", role=c("aut")),
    person("Emanuel", "Schwarz", role=c("aut")))
Author: Junfang Chen, Dietmar Lippold, Emanuel Schwarz
Maintainer: Junfang Chen <junfang.chen33@gmail.com>    
Description: Genotype imputation is essential for genome-wide association studies 
    (GWAS) to retrieve information of untyped variants and facilitate comparability 
    across studies. Based on widely used and freely available tools, 
    we have developed Gimpute, an automated processing and imputation pipeline 
    for genome-wide association data. Gimpute includes processing steps for 
    genotype liftOver, quality control, population outlier detection, 
    haplotype pre-phasing, imputation, post imputation, data management 
    and the extension to other existing pipeline. 
License: GPL-3
Imports:
    doParallel, lattice, grDevices, utils
Depends: R (>= 3.5.0)
Suggests: BiocStyle, knitr 
VignetteBuilder: knitr
biocViews: Genetics, GenomicVariation, SNP, GenomeWideAssociation, QualityControl, VariantDetection, Alignment
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1

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[mtmorgan]

I appreciate the effort that you have put into your package. However, the 'workflow' style package that has extensive system dependencies on software that is itself complex is not suitable for Bioconductor; the workflow will be challenging to build and maintain, and there is little opportunity for interoperability with existing Bioconductor software. For these reasons, I am declining this package.