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

Quick introduction is available: [http://seqminer.genomic.codes/].

Install the latest stable version:

install.packages("seqminer")

Install the development version (devtools package is required):

devtools::install_github("zhanxw/seqminer")

Citation:

Zhan, X. and Liu, D. J. (2015), SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations. Genet. Epidemiol., 39: 619–623. doi:10.1002/gepi.21918

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Reference manual

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install.packages("seqminer")

8.2 by Xiaowei Zhan, 25 days ago

http://zhanxw.github.io/seqminer/

Report a bug at https://github.com/zhanxw/seqminer/issues

Browse source code at https://github.com/cran/seqminer

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 (GRL) [cph] , Facebook , Inc [cph]

Documentation:   PDF Manual  

GPL | file LICENSE license

Suggests testthat, SKAT

System requirements: C++11, zlib headers and libraries, GNU make, optionally also bzip2 and POSIX-compliant regex functions.

Imported by sequenza, sumFREGAT.

Depended on by GenoScan, GhostKnockoff, KnockoffScreen, WGScan.

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