Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.

Documentation

Manual: seqminer.pdf
Vignette: None available.

Maintainer: Xiaowei Zhan <zhanxw at gmail.com>

Author(s): Xiaowei Zhan*, Dajiang Liu*, Attractive Chaos* (We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3 at live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.), Broad Institute / Massachusetts Institute of Technology*, Genome Research Ltd (GRL)*

Install package and any missing dependencies by running this line in your R console:

install.packages("seqminer")

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Suggests testthat, SKAT
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Package seqminer
Materials
URL http://seqminer.genomic.codes
Task Views
Version 6.0
Published 2017-05-05
License GPL | file LICENSE
BugReports https://github.com/zhanxw/seqminer/issues
SystemRequirements zlib headers and libraries, optionally also bzip2 and POSIX-compliant regex functions.
NeedsCompilation yes
Citation
CRAN checks seqminer check results
Package source seqminer_6.0.tar.gz