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 <[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 (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 <[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. |
| 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 |