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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: | 9.4 |
| Suggests: | testthat, SKAT |
| Published: | 2024-02-03 |
| 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 | file LICENSE [expanded from: GPL | file LICENSE] |
| 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. |
| 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 |
| Reference manual: | seqminer.pdf |
| Package source: | seqminer_9.4.tar.gz |
| Windows binaries: | r-devel: seqminer_9.4.zip, r-release: seqminer_9.4.zip, r-oldrel: seqminer_9.4.zip |
| macOS binaries: | r-release (arm64): seqminer_9.4.tgz, r-oldrel (arm64): seqminer_9.4.tgz, r-release (x86_64): seqminer_9.4.tgz, r-oldrel (x86_64): seqminer_9.4.tgz |
| Old sources: | seqminer archive |
| Reverse depends: | GenoScan, GhostKnockoff, KnockoffScreen, WGScan |
| Reverse imports: | Moonlight2R, sumFREGAT |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.