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.

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Description file content

Package
seqminer
Type
Package
Title
Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Version
6.7
Date
2018-12-04
Maintainer
Xiaowei Zhan
Description
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.
Copyright
We have used the following software and made minimal necessary changes: tabix, Heng Li (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.
License
GPL | file LICENSE
URL
BugReports
https://github.com/zhanxw/seqminer/issues
Packaged
2018-12-04 16:32:59 UTC; zhanxw
Repository
CRAN
Suggests
testthat, SKAT
SystemRequirements
C++11, zlib headers and libraries, GNU make, optionally also bzip2 and POSIX-compliant regex functions.
NeedsCompilation
yes
RoxygenNote
6.1.1
Encoding
UTF-8
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 (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]
Date/Publication
2018-12-06 22:10:04 UTC

install.packages('seqminer')

6.7

3 days ago

http://seqminer.genomic.codes

Xiaowei Zhan

GPL | file LICENSE

Suggests

testthat, SKAT

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