Files in seqminer
Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

configure

MD5

ChangeLog

README.md

NAMESPACE

configure.ac

DESCRIPTION

LICENSE

configure.win

cleanup

R/genMakefile.R R/seqminer.R

src/BGenFile.cpp

src/Makevars.win

src/AnnotationString.h

src/SimpleMatrix.cpp

src/VCFOutputFile.h

src/AnnotationResult.h

src/PatternMatch.h

src/vcf2genoLoader.h

src/Gene.h

src/VCFIndividual.h

src/VCFFunction.h

src/GeneLoader.h

src/PlinkOutputFile.h

src/kstring.h

src/VCFBuffer.h

src/VCFInputFile.h

src/Utils.cpp

src/CommonFunction.h

src/VCFHeader.h

src/OrderedMap.h

src/TabixReader.h

src/FileIO.cpp

src/BCFReader.cpp

src/SingleChromosomeVCFIndex.h

src/AnnotationOutput.h

src/Exception.h

src/Priority.h

src/bcf.c

src/AnnotationOutputFile.h

src/TimeUtil.h

src/SimpleMatrix.h

src/AnnotationResultCollection.h

src/PlinkOutputFile.cpp

src/FileIO.h

src/VCFConstant.h

src/VCFRecord.h

src/PatternMatch.cpp

src/SingleChromosomeVCFIndex.cpp

src/kstring.c

src/Common.h

src/tabixLoader.cpp

src/bgen2genoLoader.h

src/VCFUtil.h

src/BGenIndex.h

src/GenomeScore.h

src/GeneFormat.h

src/bcf_index.c

src/Range.h

src/SequenceUtil.h

src/BCFReader.h

src/bam_endian.h

src/FreqTable.h

src/scbcf2genoLoader.h

src/AnnotationController.h

src/StringTemplate.h

src/VCFHeader.cpp

src/LogFile.h

src/bedidx.c

src/PeopleSet.cpp

src/scbcf2genoLoader.cpp

src/ksort.h

src/RangeList.h

src/vcf2genoLoader.cpp

src/bcfutils.c

src/MmapFile.h

src/VCFIndividual.cpp

src/StringUtil.h

src/PeopleSet.h

src/knetfile.h

src/R_CPP_interface.h

src/plink2genoLoader.cpp

src/RangeList.cpp

src/GeneLoader.cpp

src/bgzf.h

src/Utils.h

src/VCFInfo.cpp

src/BGenVariant.cpp

src/VCFValue.h

src/tabix.h

src/Maximum.h

src/bcf.h

src/TypeConversion.h

src/SimpleTimer.h

src/rvMetaLoader.h

src/Indexer.h

src/Rannotation.h

src/PlinkInputFile.cpp

src/VCFUtil.cpp

src/VCFExtractor.h

src/plink2genoLoader.h

src/GeneAnnotation.h

src/TabixData.h

src/BCFHeader.h

src/HiCExtract.h

src/BGenVariant.h

src/Profiler.h

src/Type.h

src/scvcf2genoLoader.h

src/TypeConversion.cpp

src/tabix_index.c

src/khash.h

src/Profiler.cpp

src/tabixLoader.h

src/Makevars.in

src/bgen2genoLoader.cpp

src/scvcf2genoLoader.cpp

src/SingleChromosomeBCFIndex.cpp

src/VCFFilter.h

src/VCFInfo.h

src/Exception.cpp

src/config.h.in

src/rvMetaLoader.cpp

src/PlinkInputFile.h

src/BGenFile.h

src/ModelParser.h

src/SingleChromosomeBCFIndex.h

src/bgzf.c

src/BGenIndex.cpp

src/VCFInputFile.cpp

src/AnnotationInputFile.h

src/vcf.c

src/GenomeSequence.h

src/MmapFile.cpp

src/Rannotation.cpp

src/knetfile.c

src/FileFormat.h

src/seqForStat.c

src/seqminer_init.c

src/BedReader.h

src/R_CPP_interface.cpp

src/Codon.h

src/kseq.h

src/seqminer.c

src/BitReader.h

src/zstd/CONTRIBUTING.md src/zstd/README.md src/zstd/CODE_OF_CONDUCT.md

src/zstd/LICENSE

src/zstd/COPYING

src/zstd/appveyor.yml

src/zstd/TESTING.md

src/zstd/Makefile

src/zstd/build/README.md

src/zstd/build/VS2010/zstd.sln

src/zstd/build/VS2010/CompileAsCpp.props

src/zstd/build/VS2010/zstd/zstd.vcxproj

src/zstd/build/VS2010/zstd/zstd.rc

src/zstd/build/VS2010/datagen/datagen.vcxproj

src/zstd/build/VS2010/fullbench-dll/fullbench-dll.vcxproj

src/zstd/build/VS2010/libzstd/libzstd.vcxproj

src/zstd/build/VS2010/fuzzer/fuzzer.vcxproj

src/zstd/build/VS2010/libzstd-dll/libzstd-dll.vcxproj

src/zstd/build/VS2010/libzstd-dll/libzstd-dll.rc

src/zstd/build/VS2010/fullbench/fullbench.vcxproj

src/zstd/build/VS_scripts/build.VS2015.cmd

src/zstd/build/VS_scripts/build.VS2017Professional.cmd

src/zstd/build/VS_scripts/build.generic.cmd

src/zstd/build/VS_scripts/build.VS2017Enterprise.cmd

src/zstd/build/VS_scripts/README.md

src/zstd/build/VS_scripts/build.VS2012.cmd

src/zstd/build/VS_scripts/build.VS2010.cmd

src/zstd/build/VS_scripts/build.VS2017.cmd

src/zstd/build/VS_scripts/build.VS2017Community.cmd

src/zstd/build/VS_scripts/build.VS2013.cmd

src/zstd/build/VS2008/zstd.sln

src/zstd/build/VS2008/zstd/zstd.vcproj

src/zstd/build/VS2008/fuzzer/fuzzer.vcproj

src/zstd/build/VS2008/fullbench/fullbench.vcproj

src/zstd/build/VS2008/zstdlib/zstdlib.vcproj

src/zstd/build/cmake/CMakeLists.txt

src/zstd/build/cmake/contrib/CMakeLists.txt

src/zstd/build/cmake/contrib/pzstd/CMakeLists.txt

src/zstd/build/cmake/contrib/gen_html/CMakeLists.txt

src/zstd/build/cmake/tests/CMakeLists.txt

src/zstd/build/cmake/lib/CMakeLists.txt

src/zstd/build/cmake/lib/pkgconfig.cmake

src/zstd/build/cmake/lib/cmake_uninstall.cmake.in

src/zstd/build/cmake/programs/CMakeLists.txt

src/zstd/build/cmake/CMakeModules/GetZstdLibraryVersion.cmake

src/zstd/build/cmake/CMakeModules/AddZstdCompilationFlags.cmake

src/zstd/lib/libzstd.pc.in

src/zstd/lib/BUCK

src/zstd/lib/README.md

src/zstd/lib/zstd.h

src/zstd/lib/legacy/zstd_v02.c

src/zstd/lib/legacy/zstd_v07.c

src/zstd/lib/legacy/zstd_v01.h

src/zstd/lib/legacy/zstd_v03.h

src/zstd/lib/legacy/zstd_v01.c

src/zstd/lib/legacy/zstd_v05.c

src/zstd/lib/legacy/zstd_v05.h

src/zstd/lib/legacy/zstd_v06.c

src/zstd/lib/legacy/zstd_v06.h

src/zstd/lib/legacy/zstd_v04.c

src/zstd/lib/legacy/zstd_v07.h

src/zstd/lib/legacy/zstd_v03.c

src/zstd/lib/legacy/zstd_v04.h

src/zstd/lib/legacy/zstd_legacy.h

src/zstd/lib/legacy/zstd_v02.h

src/zstd/lib/dictBuilder/divsufsort.h

src/zstd/lib/dictBuilder/zdict.h

src/zstd/lib/dictBuilder/cover.h

src/zstd/lib/dictBuilder/zdict.c

src/zstd/lib/dictBuilder/divsufsort.c

src/zstd/lib/dictBuilder/cover.c

src/zstd/lib/dictBuilder/fastcover.c

src/zstd/lib/deprecated/zbuff_common.c

src/zstd/lib/deprecated/zbuff_compress.c

src/zstd/lib/deprecated/zbuff.h

src/zstd/lib/deprecated/zbuff_decompress.c

src/zstd/lib/decompress/huf_decompress.c

src/zstd/lib/decompress/zstd_decompress.c

src/zstd/lib/dll/libzstd.def

src/zstd/lib/dll/example/build_package.bat

src/zstd/lib/dll/example/README.md

src/zstd/lib/dll/example/fullbench-dll.vcxproj

src/zstd/lib/dll/example/fullbench-dll.sln

src/zstd/lib/dll/example/Makefile

src/zstd/lib/common/zstd_errors.h

src/zstd/lib/common/xxhash.h

src/zstd/lib/common/huf.h

src/zstd/lib/common/error_private.h

src/zstd/lib/common/bitstream.h

src/zstd/lib/common/threading.c

src/zstd/lib/common/xxhash.c

src/zstd/lib/common/entropy_common.c

src/zstd/lib/common/mem.h

src/zstd/lib/common/pool.h

src/zstd/lib/common/debug.c

src/zstd/lib/common/fse.h

src/zstd/lib/common/debug.h

src/zstd/lib/common/threading.h

src/zstd/lib/common/zstd_common.c

src/zstd/lib/common/zstd_internal.h

src/zstd/lib/common/compiler.h

src/zstd/lib/common/pool.c

src/zstd/lib/common/cpu.h

src/zstd/lib/common/fse_decompress.c

src/zstd/lib/common/error_private.c

src/zstd/lib/compress/huf_compress.c

src/zstd/lib/compress/zstdmt_compress.c

src/zstd/lib/compress/zstd_double_fast.c

src/zstd/lib/compress/zstd_compress.c

src/zstd/lib/compress/hist.c

src/zstd/lib/compress/zstd_opt.c

src/zstd/lib/compress/zstd_ldm.h

src/zstd/lib/compress/zstd_compress_internal.h

src/zstd/lib/compress/zstd_opt.h

src/zstd/lib/compress/zstd_lazy.c

src/zstd/lib/compress/zstd_double_fast.h

src/zstd/lib/compress/zstd_ldm.c

src/zstd/lib/compress/zstd_fast.c

src/zstd/lib/compress/zstd_lazy.h

src/zstd/lib/compress/zstdmt_compress.h

src/zstd/lib/compress/zstd_fast.h

src/zstd/lib/compress/fse_compress.c

src/zstd/lib/compress/hist.h

src/sqlite/sqlite3.c

src/sqlite/shell.c

src/sqlite/sqlite3ext.h

src/sqlite/sqlite3.h

inst/CITATION

inst/vcf/all.anno.filtered.extract.vcf.gz.scIdx

inst/vcf/all.anno.filtered.extract.headerFixed.bcf.gz

inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi

inst/vcf/all.anno.filtered.extract.headerFixed.bcf.gz.scIdx

inst/vcf/all.anno.filtered.extract.vcf.gz

inst/vcf/all.anno.filtered.extract.bcf.gz

inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz

inst/vcf/all.anno.filtered.extract.vcf.gz.tbi

inst/vcf/all.anno.filtered.extract.headerFixed.vcf.gz

inst/vcf/refFlat_hg19_6col.txt.gz

inst/vcf/all.anno.filtered.extract.bcf.gz.bci

inst/tests/correct.Rdata

inst/bgen/all.anno.filtered.extract.bgen

inst/bgen/all.anno.filtered.extract.bgen.bgi

inst/plink/all.anno.filtered.extract.bed

inst/plink/all.anno.filtered.extract.bim

inst/plink/all.anno.filtered.extract.fam

inst/tabanno/test.fa.fai

inst/tabanno/input.test.plain.txt

inst/tabanno/input.demo.vcf

inst/tabanno/test.dbNSFP.gz.tbi

inst/tabanno/codon.txt

inst/tabanno/test.bed

inst/tabanno/priority.epact.txt

inst/tabanno/test.gene.txt

inst/tabanno/test.dbNSFP.gz

inst/tabanno/priority.txt

inst/tabanno/input.test.vcf

inst/tabanno/tmp.vcf

inst/tabanno/test.fa

inst/tabanno/input.100.vcf.gz

inst/benchmark/output.png

inst/benchmark/seqminer2_benchmark_script.txt

inst/test-triallelic/test2.study1.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study2.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study3.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study1.MetaCov.assoc.gz.tbi

inst/test-triallelic/bi.MetaCov.assoc.gz.tbi

inst/test-triallelic/tri.MetaCov.assoc.gz.tbi

inst/test-triallelic/bi.MetaScore.assoc.gz

inst/test-triallelic/tri.MetaCov.assoc.gz

inst/test-triallelic/bi.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study1.MetaCov.assoc.gz

inst/test-triallelic/tri.MetaScore.assoc.gz.tbi

inst/test-triallelic/tri.MetaScore.assoc.gz

inst/test-triallelic/test2.study3.MetaCov.assoc.gz

inst/test-triallelic/test2.study2.MetaScore.assoc.gz

inst/test-triallelic/bi.MetaCov.assoc.gz

inst/test-triallelic/test2.study3.MetaScore.assoc.gz

inst/test-triallelic/test2.study3.MetaCov.assoc.gz.tbi

inst/test-triallelic/test2.study2.MetaCov.assoc.gz

inst/test-triallelic/test2.study2.MetaCov.assoc.gz.tbi

inst/test-triallelic/test2.study1.MetaScore.assoc.gz

inst/rvtests/rvtest.MetaCov.assoc.gz.tbi

inst/rvtests/rvtest.MetaScore.assoc.anno.gz.tbi

inst/rvtests/rvtest.MetaSkew.assoc.gz.tbi

inst/rvtests/rvtest.MetaCov.assoc.gz

inst/rvtests/rvtest.MetaScore.assoc.gz.tbi

inst/rvtests/rvtest.MetaSkew.assoc.gz

inst/rvtests/rvtest.MetaScore.assoc.gz

inst/rvtests/rvtest.MetaScore.assoc.anno.gz

inst/rvtests/cfh.refFlat.txt

demo/meta.workflow.R

demo/00Index

demo/vcf.workflow.R demo/annotate.R tests/testthat.R tests/testthat/test-vcf.R tests/testthat/test-triallelic.R man/verifyFilename.Rd man/createSingleChromosomeBCFIndex.Rd man/createSingleChromosomeVCFIndex.Rd man/sub-.PlinkFile.Rd man/tabix.createIndex.Rd man/readVCFToListByRange.Rd man/isDirWritable.Rd man/getCovPair.Rd man/readBGENToListByRange.Rd man/download.annotation.resource.Rd man/writeWorkflow.Rd man/readVCFToListByGene.Rd man/isInRange.Rd man/getRefBase.Rd man/readVCFToMatrixByGene.Rd man/rvmeta.readNullModel.Rd man/newJob.Rd man/annotateVcf.Rd man/validateAnnotationParameter.Rd man/annotatePlain.Rd man/annotateGene.Rd man/tabix.read.Rd man/addJob.Rd man/readSingleChromosomeBCFToMatrixByRange.Rd man/readBGENToListByGene.Rd man/rvmeta.readCovByRange.Rd man/rvmeta.writeScoreData.Rd man/tabix.read.header.Rd man/tabix.read.table.Rd man/rvmeta.readSkewByRange.Rd man/tabix.createIndex.vcf.Rd man/readVCFToMatrixByRange.Rd man/readPlinkToMatrixByIndex.Rd man/isURL.Rd man/openPlink.Rd man/hasIndex.Rd man/readBGENToMatrixByGene.Rd man/newWorkflow.Rd man/readBGENToMatrixByRange.Rd man/rvmeta.writeCovData.Rd man/SEQMINER.Rd man/makeAnnotationParameter.Rd man/rvmeta.readScoreByRange.Rd man/rvmeta.readDataByRange.Rd man/readSingleChromosomeVCFToMatrixByRange.Rd man/rvmeta.readDataByGene.Rd man/isTabixRange.Rd man/tabix.createIndex.meta.Rd

seqminer documentation built on Oct. 7, 2024, 1:15 a.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

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

Files in seqminer
Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in seqminer Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in seqminer
Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R