SeqArray: Big Data Management of Whole-genome Sequence Variant Calls

Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

AuthorXiuwen Zheng [aut, cre], Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb]
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.14.0
http://github.com/zhengxwen/SeqArray

View on Bioconductor

Files in this package

SeqArray/DESCRIPTION
SeqArray/NAMESPACE
SeqArray/NEWS
SeqArray/R
SeqArray/R/AllClasses.R SeqArray/R/AllGenerics.R SeqArray/R/ConvVCF2GDS.R SeqArray/R/Conversion.R SeqArray/R/Internal.R SeqArray/R/Methods-SeqVarGDSClass.R SeqArray/R/Methods.R SeqArray/R/Summary.R SeqArray/R/Utilities.R SeqArray/R/UtilsExport.R SeqArray/R/UtilsMerge.R
SeqArray/README.md
SeqArray/TODO
SeqArray/build
SeqArray/build/vignette.rds
SeqArray/data
SeqArray/data/KG_P1_SampData.RData
SeqArray/inst
SeqArray/inst/doc
SeqArray/inst/doc/OverviewSlides.Rmd
SeqArray/inst/doc/OverviewSlides.html
SeqArray/inst/doc/R_Integration.R
SeqArray/inst/doc/R_Integration.Rmd
SeqArray/inst/doc/R_Integration.html
SeqArray/inst/doc/SeqArrayTutorial.R
SeqArray/inst/doc/SeqArrayTutorial.Rmd
SeqArray/inst/doc/SeqArrayTutorial.html
SeqArray/inst/extdata
SeqArray/inst/extdata/1KG_phase1_release_v3_chr22.gds
SeqArray/inst/extdata/CEU_Exon.gds
SeqArray/inst/extdata/CEU_Exon.vcf.gz
SeqArray/inst/unitTests
SeqArray/inst/unitTests/data
SeqArray/inst/unitTests/data/Valid.RData
SeqArray/inst/unitTests/test_asVCF.R
SeqArray/inst/unitTests/test_c.R
SeqArray/inst/unitTests/test_cpp.R
SeqArray/inst/unitTests/test_examples.R
SeqArray/inst/unitTests/test_func.R
SeqArray/inst/unitTests/test_utils.R
SeqArray/man
SeqArray/man/KG_P1_SampData.Rd SeqArray/man/SeqArray-package.Rd SeqArray/man/SeqVarGDSClass-class.Rd SeqArray/man/seqAlleleFreq.Rd SeqArray/man/seqApply.Rd SeqArray/man/seqBED2GDS.Rd SeqArray/man/seqBlockApply.Rd SeqArray/man/seqClose.Rd SeqArray/man/seqDelete.Rd SeqArray/man/seqDigest.Rd SeqArray/man/seqExampleFileName.Rd SeqArray/man/seqExport.Rd SeqArray/man/seqGDS2SNP.Rd SeqArray/man/seqGDS2VCF.Rd SeqArray/man/seqGetData.Rd SeqArray/man/seqGetFilter.Rd SeqArray/man/seqMerge.Rd SeqArray/man/seqMissing.Rd SeqArray/man/seqNumAllele.Rd SeqArray/man/seqOpen.Rd SeqArray/man/seqOptimize.Rd SeqArray/man/seqParallel.Rd SeqArray/man/seqParallelSetup.Rd SeqArray/man/seqSNP2GDS.Rd SeqArray/man/seqSetFilter.Rd SeqArray/man/seqStorageOption.Rd SeqArray/man/seqSummary.Rd SeqArray/man/seqSystem.Rd SeqArray/man/seqTranspose.Rd SeqArray/man/seqVCF2GDS.Rd SeqArray/man/seqVCF_Header.Rd SeqArray/man/seqVCF_SampID.Rd
SeqArray/src
SeqArray/src/ConvGDS2VCF.cpp
SeqArray/src/ConvToGDS.cpp
SeqArray/src/ConvVCF2GDS.cpp
SeqArray/src/FileMerge.cpp
SeqArray/src/GetData.cpp
SeqArray/src/Index.cpp
SeqArray/src/Index.h
SeqArray/src/LinkSNPRelate.cpp
SeqArray/src/Makevars
SeqArray/src/Methods.cpp
SeqArray/src/R_SeqArray.c
SeqArray/src/ReadBySample.cpp
SeqArray/src/ReadBySample.h
SeqArray/src/ReadByVariant.cpp
SeqArray/src/ReadByVariant.h
SeqArray/src/SeqArray.cpp
SeqArray/src/pkg_test.cpp
SeqArray/src/vectorization.c
SeqArray/src/vectorization.h
SeqArray/tests
SeqArray/tests/test.R
SeqArray/vignettes
SeqArray/vignettes/OverviewSlides.Rmd
SeqArray/vignettes/R_Integration.Rmd
SeqArray/vignettes/SeqArrayTutorial.Rmd
SeqArray/vignettes/link.png
SeqArray/vignettes/seqarray_bib.bib
SeqArray/vignettes/seqarray_workflow.png

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