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 | fileLICENSE [expanded from: GPL | file LICENSE] |
| Copyright: | We have used the following software and made minimalnecessary changes: tabix, Heng Li <lh3@live.co.uk> (MITlicense), SQLite (Public Domain), Zstandard (BSD license). Fortabix, we removed standard IO related functions, e.g. printf,fprintf ; also changed its un-safe pointer arithmetics. Forzstandard, we removed compiler (clang, MSVC) specificpreprocessing 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[issues need fixing before 2025-12-22] |