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:	9.7
Suggests:	testthat, SKAT
Published:	2024-10-02
DOI:	10.32614/CRAN.package.seqminer
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], D. Richard Hipp [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 (BSD 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://zhanxw.github.io/seqminer/
NeedsCompilation:	yes
SystemRequirements:	C++17, 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

Documentation:

Reference manual:

seqminer.pdf

Downloads:

Package source:	seqminer_9.7.tar.gz
Windows binaries:	r-devel: seqminer_9.7.zip, r-release: seqminer_9.7.zip, r-oldrel: seqminer_9.7.zip
macOS binaries:	r-release (arm64): seqminer_9.7.tgz, r-oldrel (arm64): seqminer_9.7.tgz, r-release (x86_64): seqminer_9.7.tgz, r-oldrel (x86_64): seqminer_9.7.tgz
Old sources:	seqminer archive

Reverse dependencies:

Reverse depends:	GenoScan, GhostKnockoff, KnockoffScreen, WGScan
Reverse imports:	Moonlight2R, sumFREGAT

Linking:

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