seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

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/BGEN 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.

Version: 6.7
Suggests: testthat, SKAT
Published: 2018-12-06
Author: Xiaowei Zhan [aut, cre], Dajiang Liu [aut], Attractive Chaos [cph] (We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@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 [cph], Genome Research Ltd (GRL) [cph], Facebook, Inc [cph]
Maintainer: Xiaowei Zhan <zhanxw at gmail.com>
BugReports: https://github.com/zhanxw/seqminer/issues
License: GPL-2 | GPL-3 | file LICENSE [expanded from: GPL | file LICENSE]
Copyright: We have used the following software and made minimal necessary changes: tabix, Heng Li <lh3@live.co.uk> (MIT license), SQLite (Public Domain), Zstandard (MIT license). For tabix, we removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics. For zstandard, we removed compiler (clang, MSVC) specific preprocessing flags.
URL: http://seqminer.genomic.codes
NeedsCompilation: yes
SystemRequirements: C++11, zlib headers and libraries, GNU make, optionally also bzip2 and POSIX-compliant regex functions.
Citation: seqminer citation info
Materials: README ChangeLog
CRAN checks: seqminer results

Downloads:

Reference manual: seqminer.pdf
Package source: seqminer_6.7.tar.gz
Windows binaries: r-devel: seqminer_6.7.zip, r-release: seqminer_6.7.zip, r-oldrel: seqminer_6.7.zip
OS X binaries: r-release: seqminer_6.7.tgz, r-oldrel: seqminer_6.7.tgz
Old sources: seqminer archive

Reverse dependencies:

Reverse imports: sumFREGAT
Reverse suggests: FREGAT

Linking:

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