CRAN/E | seqminer

seqminer

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

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 <[email protected]> (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 2024-02-03 169 days ago
Needs compilation? yes
License GPL-2
License GPL-3
License File
CRAN checks seqminer results

Downloads

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Maintainer

Maintainer

Xiaowei Zhan

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 <[email protected]> (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

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Reverse Depends

GenoScan
GhostKnockoff
KnockoffScreen
WGScan

Reverse Imports

Moonlight2R
sumFREGAT