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

cleanup
MD5
configure.ac
LICENSE
DESCRIPTION
README.md
NAMESPACE
configure.win
configure
ChangeLog
inst/CITATION
inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi
inst/vcf/all.anno.filtered.extract.vcf.gz.tbi
inst/vcf/all.anno.filtered.extract.bcf.gz.bci
inst/vcf/all.anno.filtered.extract.bcf.gz
inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz
inst/vcf/refFlat_hg19_6col.txt.gz
inst/vcf/all.anno.filtered.extract.vcf.gz
inst/rvtests/cfh.refFlat.txt
inst/rvtests/rvtest.MetaSkew.assoc.gz.tbi
inst/rvtests/rvtest.MetaSkew.assoc.gz
inst/rvtests/rvtest.MetaScore.assoc.anno.gz.tbi
inst/rvtests/rvtest.MetaScore.assoc.gz
inst/rvtests/rvtest.MetaScore.assoc.gz.tbi
inst/rvtests/rvtest.MetaCov.assoc.gz
inst/rvtests/rvtest.MetaCov.assoc.gz.tbi
inst/rvtests/rvtest.MetaScore.assoc.anno.gz
inst/doc/Manual.html
inst/bgen/all.anno.filtered.extract.bgen
inst/bgen/all.anno.filtered.extract.bgen.bgi
inst/test-triallelic/test2.study2.MetaScore.assoc.gz.tbi
inst/test-triallelic/test2.study1.MetaScore.assoc.gz
inst/test-triallelic/test2.study1.MetaCov.assoc.gz.tbi
inst/test-triallelic/test2.study1.MetaScore.assoc.gz.tbi
inst/test-triallelic/test2.study3.MetaCov.assoc.gz
inst/test-triallelic/tri.MetaCov.assoc.gz
inst/test-triallelic/bi.MetaScore.assoc.gz.tbi
inst/test-triallelic/tri.MetaScore.assoc.gz.tbi
inst/test-triallelic/test2.study2.MetaScore.assoc.gz
inst/test-triallelic/test2.study3.MetaScore.assoc.gz.tbi
inst/test-triallelic/tri.MetaCov.assoc.gz.tbi
inst/test-triallelic/test2.study1.MetaCov.assoc.gz
inst/test-triallelic/test2.study2.MetaCov.assoc.gz
inst/test-triallelic/test2.study3.MetaCov.assoc.gz.tbi
inst/test-triallelic/test2.study2.MetaCov.assoc.gz.tbi
inst/test-triallelic/bi.MetaCov.assoc.gz.tbi
inst/test-triallelic/bi.MetaCov.assoc.gz
inst/test-triallelic/tri.MetaScore.assoc.gz
inst/test-triallelic/bi.MetaScore.assoc.gz
inst/test-triallelic/test2.study3.MetaScore.assoc.gz
inst/tabanno/input.test.vcf
inst/tabanno/tmp.vcf
inst/tabanno/priority.epact.txt
inst/tabanno/test.bed
inst/tabanno/test.dbNSFP.gz.tbi
inst/tabanno/test.fa.fai
inst/tabanno/test.gene.txt
inst/tabanno/input.demo.vcf
inst/tabanno/codon.txt
inst/tabanno/test.dbNSFP.gz
inst/tabanno/input.100.vcf.gz
inst/tabanno/test.fa
inst/tabanno/input.test.plain.txt
inst/tabanno/priority.txt
inst/plink/all.anno.filtered.extract.bed
inst/plink/all.anno.filtered.extract.bim
inst/plink/all.anno.filtered.extract.fam
inst/tests/correct.Rdata
demo/meta.workflow.R demo/annotate.R demo/vcf.workflow.R
demo/00Index
R/seqminer.R R/genMakefile.R
src/Maximum.h
src/AnnotationResultCollection.h
src/kseq.h
src/tabix_index.c
src/ksort.h
src/FileFormat.h
src/VCFInputFile.cpp
src/BCFReader.h
src/vcf2genoLoader.cpp
src/bgen2genoLoader.cpp
src/AnnotationOutput.h
src/BedReader.h
src/GeneLoader.h
src/VCFFunction.h
src/CommonFunction.h
src/Exception.h
src/StringTemplate.h
src/FileIO.cpp
src/AnnotationString.h
src/kstring.c
src/Utils.h
src/bcf.c
src/VCFInputFile.h
src/knetfile.h
src/VCFBuffer.h
src/bedidx.c
src/SequenceUtil.h
src/R_CPP_interface.cpp
src/VCFIndividual.h
src/PlinkOutputFile.h
src/Makevars.win
src/rvMetaLoader.h
src/GenomeSequence.h
src/bcf_index.c
src/BGenIndex.cpp
src/BGenVariant.cpp
src/tabix.h
src/bgzf.c
src/GeneLoader.cpp
src/bgen2genoLoader.h
src/kstring.h
src/BCFReader.cpp
src/FreqTable.h
src/bam_endian.h
src/Common.h
src/LogFile.h
src/bcf.h
src/Rannotation.h
src/VCFHeader.cpp
src/AnnotationResult.h
src/GeneFormat.h
src/AnnotationInputFile.h
src/OrderedMap.h
src/SimpleTimer.h
src/TimeUtil.h
src/Profiler.cpp
src/Profiler.h
src/PatternMatch.h
src/VCFRecord.h
src/Type.h
src/khash.h
src/Gene.h
src/BGenFile.cpp
src/TypeConversion.h
src/bgzf.h
src/VCFInfo.cpp
src/Rannotation.cpp
src/GenomeScore.h
src/AnnotationController.h
src/rvMetaLoader.cpp
src/knetfile.c
src/Codon.h
src/config.h.in
src/VCFHeader.h
src/GeneAnnotation.h
src/BGenIndex.h
src/FileIO.h
src/PeopleSet.cpp
src/VCFInfo.h
src/Indexer.h
src/ModelParser.h
src/VCFConstant.h
src/R_CPP_interface.h
src/VCFUtil.h
src/PlinkInputFile.cpp
src/VCFExtractor.h
src/seqForStat.c
src/seqminer.c
src/vcf2genoLoader.h
src/Makevars.in
src/SimpleMatrix.cpp
src/Priority.h
src/BGenFile.h
src/TabixData.h
src/PlinkOutputFile.cpp
src/Utils.cpp
src/tabixLoader.h
src/VCFFilter.h
src/plink2genoLoader.cpp
src/StringUtil.h
src/PatternMatch.cpp
src/HiCExtract.h
src/SimpleMatrix.h
src/VCFValue.h
src/VCFIndividual.cpp
src/VCFUtil.cpp
src/seqminer_init.c
src/TypeConversion.cpp
src/bcfutils.c
src/plink2genoLoader.h
src/RangeList.cpp
src/PlinkInputFile.h
src/PeopleSet.h
src/BitReader.h
src/RangeList.h
src/TabixReader.h
src/tabixLoader.cpp
src/vcf.c
src/Exception.cpp
src/AnnotationOutputFile.h
src/VCFOutputFile.h
src/Range.h
src/BGenVariant.h
src/sqlite/sqlite3.h
src/sqlite/sqlite3ext.h
src/sqlite/sqlite3.c
src/sqlite/shell.c
src/zstd/Makefile
src/zstd/CODE_OF_CONDUCT.md
src/zstd/COPYING
src/zstd/TESTING.md
src/zstd/file.list
src/zstd/LICENSE
src/zstd/CONTRIBUTING.md src/zstd/README.md
src/zstd/appveyor.yml
src/zstd/lib/zstd.h
src/zstd/lib/libzstd.pc.in
src/zstd/lib/README.md
src/zstd/lib/BUCK
src/zstd/lib/common/debug.h
src/zstd/lib/common/zstd_common.c
src/zstd/lib/common/xxhash.h
src/zstd/lib/common/zstd_internal.h
src/zstd/lib/common/debug.c
src/zstd/lib/common/bitstream.h
src/zstd/lib/common/error_private.h
src/zstd/lib/common/error_private.c
src/zstd/lib/common/entropy_common.c
src/zstd/lib/common/threading.h
src/zstd/lib/common/pool.c
src/zstd/lib/common/xxhash.c
src/zstd/lib/common/mem.h
src/zstd/lib/common/zstd_errors.h
src/zstd/lib/common/fse_decompress.c
src/zstd/lib/common/pool.h
src/zstd/lib/common/cpu.h
src/zstd/lib/common/threading.c
src/zstd/lib/common/compiler.h
src/zstd/lib/common/fse.h
src/zstd/lib/common/huf.h
src/zstd/lib/decompress/zstd_decompress.c
src/zstd/lib/decompress/huf_decompress.c
src/zstd/lib/compress/hist.h
src/zstd/lib/compress/zstd_fast.c
src/zstd/lib/compress/zstd_double_fast.h
src/zstd/lib/compress/hist.c
src/zstd/lib/compress/zstd_ldm.h
src/zstd/lib/compress/zstdmt_compress.h
src/zstd/lib/compress/zstd_compress_internal.h
src/zstd/lib/compress/zstd_opt.c
src/zstd/lib/compress/zstd_fast.h
src/zstd/lib/compress/zstd_compress.c
src/zstd/lib/compress/huf_compress.c
src/zstd/lib/compress/zstd_lazy.h
src/zstd/lib/compress/zstd_double_fast.c
src/zstd/lib/compress/zstd_ldm.c
src/zstd/lib/compress/zstd_opt.h
src/zstd/lib/compress/zstd_lazy.c
src/zstd/lib/compress/zstdmt_compress.c
src/zstd/lib/compress/fse_compress.c
src/zstd/lib/deprecated/zbuff.h
src/zstd/lib/deprecated/zbuff_compress.c
src/zstd/lib/deprecated/zbuff_decompress.c
src/zstd/lib/deprecated/zbuff_common.c
src/zstd/lib/legacy/zstd_v01.c
src/zstd/lib/legacy/zstd_v01.h
src/zstd/lib/legacy/zstd_v05.h
src/zstd/lib/legacy/zstd_v02.h
src/zstd/lib/legacy/zstd_v07.c
src/zstd/lib/legacy/zstd_v04.c
src/zstd/lib/legacy/zstd_v06.h
src/zstd/lib/legacy/zstd_v02.c
src/zstd/lib/legacy/zstd_v03.h
src/zstd/lib/legacy/zstd_v04.h
src/zstd/lib/legacy/zstd_v03.c
src/zstd/lib/legacy/zstd_v07.h
src/zstd/lib/legacy/zstd_v06.c
src/zstd/lib/legacy/zstd_v05.c
src/zstd/lib/legacy/zstd_legacy.h
src/zstd/lib/dll/libzstd.def
src/zstd/lib/dll/example/Makefile
src/zstd/lib/dll/example/build_package.bat
src/zstd/lib/dll/example/fullbench-dll.vcxproj
src/zstd/lib/dll/example/README.md
src/zstd/lib/dll/example/fullbench-dll.sln
src/zstd/lib/dictBuilder/zdict.h
src/zstd/lib/dictBuilder/divsufsort.c
src/zstd/lib/dictBuilder/zdict.c
src/zstd/lib/dictBuilder/cover.h
src/zstd/lib/dictBuilder/divsufsort.h
src/zstd/lib/dictBuilder/fastcover.c
src/zstd/lib/dictBuilder/cover.c
src/zstd/build/README.md
src/zstd/build/VS_scripts/build.VS2012.cmd
src/zstd/build/VS_scripts/build.generic.cmd
src/zstd/build/VS_scripts/build.VS2017.cmd
src/zstd/build/VS_scripts/build.VS2015.cmd
src/zstd/build/VS_scripts/build.VS2017Community.cmd
src/zstd/build/VS_scripts/build.VS2017Enterprise.cmd
src/zstd/build/VS_scripts/README.md
src/zstd/build/VS_scripts/build.VS2017Professional.cmd
src/zstd/build/VS_scripts/build.VS2013.cmd
src/zstd/build/VS_scripts/build.VS2010.cmd
src/zstd/build/cmake/CMakeLists.txt
src/zstd/build/cmake/lib/cmake_uninstall.cmake.in
src/zstd/build/cmake/lib/pkgconfig.cmake
src/zstd/build/cmake/lib/CMakeLists.txt
src/zstd/build/cmake/programs/CMakeLists.txt
src/zstd/build/cmake/contrib/CMakeLists.txt
src/zstd/build/cmake/contrib/gen_html/CMakeLists.txt
src/zstd/build/cmake/contrib/pzstd/CMakeLists.txt
src/zstd/build/cmake/tests/CMakeLists.txt
src/zstd/build/cmake/CMakeModules/AddZstdCompilationFlags.cmake
src/zstd/build/cmake/CMakeModules/GetZstdLibraryVersion.cmake
src/zstd/build/VS2010/CompileAsCpp.props
src/zstd/build/VS2010/zstd.sln
src/zstd/build/VS2010/libzstd/libzstd.vcxproj
src/zstd/build/VS2010/datagen/datagen.vcxproj
src/zstd/build/VS2010/libzstd-dll/libzstd-dll.rc
src/zstd/build/VS2010/libzstd-dll/libzstd-dll.vcxproj
src/zstd/build/VS2010/fullbench/fullbench.vcxproj
src/zstd/build/VS2010/fullbench-dll/fullbench-dll.vcxproj
src/zstd/build/VS2010/zstd/zstd.vcxproj
src/zstd/build/VS2010/zstd/zstd.rc
src/zstd/build/VS2010/fuzzer/fuzzer.vcxproj
src/zstd/build/VS2008/zstd.sln
src/zstd/build/VS2008/zstdlib/zstdlib.vcproj
src/zstd/build/VS2008/fullbench/fullbench.vcproj
src/zstd/build/VS2008/zstd/zstd.vcproj
src/zstd/build/VS2008/fuzzer/fuzzer.vcproj
man/tabix.createIndex.Rd man/SeqMiner.Rd man/tabix.read.Rd man/addJob.Rd man/newJob.Rd man/annotateGene.Rd man/readPlinkToMatrixByIndex.Rd man/annotateVcf.Rd man/rvmeta.writeScoreData.Rd man/rvmeta.readSkewByRange.Rd man/tabix.read.header.Rd man/annotatePlain.Rd man/readBGENToMatrixByRange.Rd man/readBGENToListByRange.Rd man/tabix.read.table.Rd man/writeWorkflow.Rd man/verifyFilename.Rd man/download.annotation.resource.Rd man/rvmeta.readDataByRange.Rd man/validateAnnotationParameter.Rd man/readVCFToListByRange.Rd man/readVCFToMatrixByRange.Rd man/readBGENToMatrixByGene.Rd man/isURL.Rd man/makeAnnotationParameter.Rd man/newWorkflow.Rd man/rvmeta.writeCovData.Rd man/readVCFToListByGene.Rd man/getRefBase.Rd man/hasIndex.Rd man/rvmeta.readScoreByRange.Rd man/tabix.createIndex.meta.Rd man/getCovPair.Rd man/openPlink.Rd man/tabix.createIndex.vcf.Rd man/readBGENToListByGene.Rd man/isInRange.Rd man/rvmeta.readCovByRange.Rd man/rvmeta.readNullModel.Rd man/readVCFToMatrixByGene.Rd man/sub-.PlinkFile.Rd man/isTabixRange.Rd man/rvmeta.readDataByGene.Rd man/isDirWritable.Rd tests/testthat.R tests/testthat/test-triallelic.R tests/testthat/test-vcf.R
seqminer documentation built on Jan. 8, 2019, 5:05 p.m.