What does the R-package 'seqminer' do?

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

Who authored seqminer?

Xiaowei Zhan, Dajiang Liu, Attractive Chaos, Broad Institute / Massachusetts Institute of Technology, Genome Research Ltd, Facebook, Inc, D. Richard Hipp

CRAN/E | seqminer

Installation

About

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.

Citation	seqminer citation info
zhanxw.github.io/seqminer/
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.
System requirements	C++17, zlib headers and libraries, GNU make, optionally also bzip2 and POSIX-compliant regex functions.
Bug report	File report

Key Metrics

Version	9.4
Published	2024-02-03 90 days ago
Needs compilation?	yes
License	GPL-2
License	GPL-3
License	File
CRAN checks	seqminer results

Downloads

Yesterday	113 0%
Last 7 days	227 -28%
Last 30 days	1.189 -18%
Last 90 days	4.038 -6%
Last 365 days	15.921 -13%

Maintainer

Xiaowei Zhan

zhanxw@gmail.com

Authors

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	cph (GRL)
Facebook
Inc	cph
D. Richard Hipp	cph

Material

README
ChangeLog
Reference manual
Package source

macOS

r-release	arm64
r-oldrel	arm64
r-release	x86_64

Windows

r-devel	x86_64
r-release	x86_64
r-oldrel	x86_64

Old Sources

seqminer archive

Suggests

testthat
SKAT

Reverse Depends

GenoScan
GhostKnockoff
KnockoffScreen
WGScan

Reverse Imports

Moonlight2R
sumFREGAT