Files in BitSeq

Transcript expression inference and differential expression analysis for RNA-seq data

configure.ac

configure

NAMESPACE

DESCRIPTION

cleanup

LICENSE

build/vignette.rds

src/common.h

src/PosteriorSamples.cpp

src/TranscriptInfo.cpp

src/GibbsSampler.h

src/GibbsParameters.cpp

src/GibbsSampler.cpp

src/estimateDE.cpp

src/Makevars.common

src/transposeFiles.h

src/transposeFiles.cpp

src/getGeneExpression.cpp

src/FileHeader.cpp

src/Makevars.win

src/ReadDistribution.h

src/CollapsedSampler.cpp

src/Makevars.in

src/getVariance.cpp

src/VariationalBayes.h

src/common.cpp

src/FileHeader.h

src/ArgumentParser.cpp

src/estimateVBExpression.cpp

src/misc.cpp

src/lowess.cpp

src/Rhtslib_bam_plbuf.c

src/ReadDistribution.cpp

src/R_init_BitSeq.cpp

src/TranscriptExpression.h

src/Rhtslib_sam.c

src/VariationalBayes.cpp

src/getWithinGeneExpression.cpp

src/Sampler.h

src/estimateHyperPar.cpp

src/MyTimer.h

src/CollapsedSampler.h

src/TranscriptSequence.h

src/GibbsParameters.h

src/Makevars.win.in

src/SimpleSparse.cpp

src/TranscriptInfo.h

src/TagAlignments.cpp

src/Sampler.cpp

src/TranscriptExpression.cpp

src/misc.h

src/parseAlignment.cpp

src/PosteriorSamples.h

src/TagAlignments.h

src/ArgumentParser.h

src/estimateExpression.cpp

src/TranscriptSequence.cpp

src/MyTimer.cpp

src/SimpleSparse.h

src/lowess.h

src/asa103/LICENSE.txt

src/asa103/asa103.hpp

src/boost/static_assert.hpp

src/boost/config.hpp

src/boost/type.hpp

src/boost/integer_fwd.hpp

src/boost/limits.hpp

src/boost/integer_traits.hpp

src/boost/assert.hpp

src/boost/integer.hpp

src/boost/cstdint.hpp

src/boost/current_function.hpp

src/boost/LICENSE_1_0.txt

src/boost/version.hpp

src/boost/README

src/boost/non_type.hpp

src/boost/config/select_platform_config.hpp

src/boost/config/user.hpp

src/boost/config/auto_link.hpp

src/boost/config/abi_suffix.hpp

src/boost/config/select_compiler_config.hpp

src/boost/config/warning_disable.hpp

src/boost/config/posix_features.hpp

src/boost/config/select_stdlib_config.hpp

src/boost/config/suffix.hpp

src/boost/config/requires_threads.hpp

src/boost/config/abi_prefix.hpp

src/boost/config/compiler/sunpro_cc.hpp

src/boost/config/compiler/common_edg.hpp

src/boost/config/compiler/cray.hpp

src/boost/config/compiler/nvcc.hpp

src/boost/config/compiler/borland.hpp

src/boost/config/compiler/kai.hpp

src/boost/config/compiler/codegear.hpp

src/boost/config/compiler/hp_acc.hpp

src/boost/config/compiler/sgi_mipspro.hpp

src/boost/config/compiler/gcc_xml.hpp

src/boost/config/compiler/gcc.hpp

src/boost/config/compiler/greenhills.hpp

src/boost/config/compiler/pgi.hpp

src/boost/config/compiler/metrowerks.hpp

src/boost/config/compiler/vacpp.hpp

src/boost/config/compiler/pathscale.hpp

src/boost/config/compiler/comeau.hpp

src/boost/config/compiler/visualc.hpp

src/boost/config/compiler/compaq_cxx.hpp

src/boost/config/compiler/digitalmars.hpp

src/boost/config/compiler/intel.hpp

src/boost/config/compiler/clang.hpp

src/boost/config/compiler/mpw.hpp

src/boost/config/platform/linux.hpp

src/boost/config/platform/bsd.hpp

src/boost/config/platform/cray.hpp

src/boost/config/platform/vms.hpp

src/boost/config/platform/cygwin.hpp

src/boost/config/platform/irix.hpp

src/boost/config/platform/hpux.hpp

src/boost/config/platform/symbian.hpp

src/boost/config/platform/beos.hpp

src/boost/config/platform/macos.hpp

src/boost/config/platform/amigaos.hpp

src/boost/config/platform/solaris.hpp

src/boost/config/platform/vxworks.hpp

src/boost/config/platform/qnxnto.hpp

src/boost/config/platform/win32.hpp

src/boost/config/platform/aix.hpp

src/boost/config/stdlib/libcpp.hpp

src/boost/config/stdlib/dinkumware.hpp

src/boost/config/stdlib/modena.hpp

src/boost/config/stdlib/libcomo.hpp

src/boost/config/stdlib/vacpp.hpp

src/boost/config/stdlib/roguewave.hpp

src/boost/config/stdlib/msl.hpp

src/boost/config/stdlib/stlport.hpp

src/boost/config/stdlib/libstdcpp3.hpp

src/boost/config/stdlib/sgi.hpp

src/boost/config/abi/borland_prefix.hpp

src/boost/config/abi/msvc_prefix.hpp

src/boost/config/abi/borland_suffix.hpp

src/boost/config/abi/msvc_suffix.hpp

src/boost/config/no_tr1/complex.hpp

src/boost/config/no_tr1/memory.hpp

src/boost/config/no_tr1/cmath.hpp

src/boost/config/no_tr1/functional.hpp

src/boost/config/no_tr1/utility.hpp

src/boost/preprocessor/empty.hpp

src/boost/preprocessor/inc.hpp

src/boost/preprocessor/comma_if.hpp

src/boost/preprocessor/iterate.hpp

src/boost/preprocessor/cat.hpp

src/boost/preprocessor/repeat.hpp

src/boost/preprocessor/enum_params.hpp

src/boost/preprocessor/identity.hpp

src/boost/preprocessor/config/config.hpp

src/boost/preprocessor/facilities/empty.hpp

src/boost/preprocessor/facilities/overload.hpp

src/boost/preprocessor/facilities/identity.hpp

src/boost/preprocessor/variadic/size.hpp

src/boost/preprocessor/variadic/elem.hpp

src/boost/preprocessor/repetition/repeat.hpp

src/boost/preprocessor/repetition/for.hpp

src/boost/preprocessor/repetition/enum_params.hpp

src/boost/preprocessor/repetition/detail/for.hpp

src/boost/preprocessor/repetition/detail/dmc/for.hpp

src/boost/preprocessor/repetition/detail/edg/for.hpp

src/boost/preprocessor/repetition/detail/msvc/for.hpp

src/boost/preprocessor/debug/error.hpp

src/boost/preprocessor/array/size.hpp

src/boost/preprocessor/array/data.hpp

src/boost/preprocessor/array/elem.hpp

src/boost/preprocessor/list/fold_right.hpp

src/boost/preprocessor/list/adt.hpp

src/boost/preprocessor/list/for_each_i.hpp

src/boost/preprocessor/list/fold_left.hpp

src/boost/preprocessor/list/reverse.hpp

src/boost/preprocessor/list/detail/fold_right.hpp

src/boost/preprocessor/list/detail/fold_left.hpp

src/boost/preprocessor/list/detail/dmc/fold_left.hpp

src/boost/preprocessor/list/detail/edg/fold_right.hpp

src/boost/preprocessor/list/detail/edg/fold_left.hpp

src/boost/preprocessor/control/iif.hpp

src/boost/preprocessor/control/if.hpp

src/boost/preprocessor/control/expr_iif.hpp

src/boost/preprocessor/control/while.hpp

src/boost/preprocessor/control/detail/while.hpp

src/boost/preprocessor/control/detail/dmc/while.hpp

src/boost/preprocessor/control/detail/edg/while.hpp

src/boost/preprocessor/control/detail/msvc/while.hpp

src/boost/preprocessor/iteration/iterate.hpp

src/boost/preprocessor/iteration/local.hpp

src/boost/preprocessor/iteration/self.hpp

src/boost/preprocessor/iteration/detail/start.hpp

src/boost/preprocessor/iteration/detail/rlocal.hpp

src/boost/preprocessor/iteration/detail/finish.hpp

src/boost/preprocessor/iteration/detail/local.hpp

src/boost/preprocessor/iteration/detail/self.hpp

src/boost/preprocessor/iteration/detail/iter/forward3.hpp

src/boost/preprocessor/iteration/detail/iter/forward1.hpp

src/boost/preprocessor/iteration/detail/iter/reverse2.hpp

src/boost/preprocessor/iteration/detail/iter/forward2.hpp

src/boost/preprocessor/iteration/detail/iter/reverse3.hpp

src/boost/preprocessor/iteration/detail/iter/reverse1.hpp

src/boost/preprocessor/iteration/detail/iter/reverse4.hpp

src/boost/preprocessor/iteration/detail/iter/forward4.hpp

src/boost/preprocessor/iteration/detail/iter/reverse5.hpp

src/boost/preprocessor/iteration/detail/iter/forward5.hpp

src/boost/preprocessor/iteration/detail/bounds/upper1.hpp

src/boost/preprocessor/iteration/detail/bounds/lower1.hpp

src/boost/preprocessor/iteration/detail/bounds/upper5.hpp

src/boost/preprocessor/iteration/detail/bounds/upper4.hpp

src/boost/preprocessor/iteration/detail/bounds/lower2.hpp

src/boost/preprocessor/iteration/detail/bounds/lower4.hpp

src/boost/preprocessor/iteration/detail/bounds/upper3.hpp

src/boost/preprocessor/iteration/detail/bounds/lower3.hpp

src/boost/preprocessor/iteration/detail/bounds/lower5.hpp

src/boost/preprocessor/iteration/detail/bounds/upper2.hpp

src/boost/preprocessor/tuple/eat.hpp

src/boost/preprocessor/tuple/rem.hpp

src/boost/preprocessor/tuple/to_list.hpp

src/boost/preprocessor/tuple/elem.hpp

src/boost/preprocessor/detail/is_binary.hpp

src/boost/preprocessor/detail/auto_rec.hpp

src/boost/preprocessor/detail/check.hpp

src/boost/preprocessor/detail/dmc/auto_rec.hpp

src/boost/preprocessor/slot/slot.hpp

src/boost/preprocessor/slot/detail/slot3.hpp

src/boost/preprocessor/slot/detail/def.hpp

src/boost/preprocessor/slot/detail/shared.hpp

src/boost/preprocessor/slot/detail/slot1.hpp

src/boost/preprocessor/slot/detail/slot5.hpp

src/boost/preprocessor/slot/detail/counter.hpp

src/boost/preprocessor/slot/detail/slot2.hpp

src/boost/preprocessor/slot/detail/slot4.hpp

src/boost/preprocessor/arithmetic/add.hpp

src/boost/preprocessor/arithmetic/inc.hpp

src/boost/preprocessor/arithmetic/sub.hpp

src/boost/preprocessor/arithmetic/dec.hpp

src/boost/preprocessor/logical/bool.hpp

src/boost/preprocessor/logical/and.hpp

src/boost/preprocessor/logical/bitand.hpp

src/boost/preprocessor/logical/compl.hpp

src/boost/preprocessor/punctuation/comma_if.hpp

src/boost/preprocessor/punctuation/comma.hpp

src/boost/mpl/integral_c.hpp

src/boost/mpl/lambda_fwd.hpp

src/boost/mpl/int_fwd.hpp

src/boost/mpl/void_fwd.hpp

src/boost/mpl/bool.hpp

src/boost/mpl/integral_c_tag.hpp

src/boost/mpl/int.hpp

src/boost/mpl/integral_c_fwd.hpp

src/boost/mpl/if.hpp

src/boost/mpl/bool_fwd.hpp

src/boost/mpl/aux_/na.hpp

src/boost/mpl/aux_/integral_wrapper.hpp

src/boost/mpl/aux_/value_wknd.hpp

src/boost/mpl/aux_/na_spec.hpp

src/boost/mpl/aux_/adl_barrier.hpp

src/boost/mpl/aux_/na_fwd.hpp

src/boost/mpl/aux_/yes_no.hpp

src/boost/mpl/aux_/nttp_decl.hpp

src/boost/mpl/aux_/static_cast.hpp

src/boost/mpl/aux_/lambda_support.hpp

src/boost/mpl/aux_/lambda_arity_param.hpp

src/boost/mpl/aux_/arity.hpp

src/boost/mpl/aux_/template_arity_fwd.hpp

src/boost/mpl/aux_/config/arrays.hpp

src/boost/mpl/aux_/config/msvc.hpp

src/boost/mpl/aux_/config/ttp.hpp

src/boost/mpl/aux_/config/preprocessor.hpp

src/boost/mpl/aux_/config/dtp.hpp

src/boost/mpl/aux_/config/ctps.hpp

src/boost/mpl/aux_/config/workaround.hpp

src/boost/mpl/aux_/config/gcc.hpp

src/boost/mpl/aux_/config/eti.hpp

src/boost/mpl/aux_/config/static_constant.hpp

src/boost/mpl/aux_/config/lambda.hpp

src/boost/mpl/aux_/config/adl.hpp

src/boost/mpl/aux_/config/intel.hpp

src/boost/mpl/aux_/config/integral.hpp

src/boost/mpl/aux_/config/nttp.hpp

src/boost/mpl/aux_/config/overload_resolution.hpp

src/boost/mpl/aux_/preprocessor/filter_params.hpp

src/boost/mpl/aux_/preprocessor/sub.hpp

src/boost/mpl/aux_/preprocessor/def_params_tail.hpp

src/boost/mpl/aux_/preprocessor/params.hpp

src/boost/mpl/aux_/preprocessor/enum.hpp

src/boost/mpl/aux_/preprocessor/tuple.hpp

src/boost/mpl/limits/arity.hpp

src/boost/detail/workaround.hpp

src/boost/detail/limits.hpp

src/boost/detail/endian.hpp

src/boost/random/mersenne_twister.hpp

src/boost/random/normal_distribution.hpp

src/boost/random/exponential_distribution.hpp

src/boost/random/uniform_01.hpp

src/boost/random/gamma_distribution.hpp

src/boost/random/detail/ptr_helper.hpp

src/boost/random/detail/config.hpp

src/boost/random/detail/generator_bits.hpp

src/boost/random/detail/seed.hpp

src/boost/random/detail/enable_warnings.hpp

src/boost/random/detail/integer_log2.hpp

src/boost/random/detail/large_arithmetic.hpp

src/boost/random/detail/disable_warnings.hpp

src/boost/random/detail/seed_impl.hpp

src/boost/random/detail/operators.hpp

src/boost/random/detail/const_mod.hpp

src/boost/random/detail/signed_unsigned_tools.hpp

src/boost/random/detail/generator_seed_seq.hpp

src/boost/integer/static_log2.hpp

src/boost/integer/integer_mask.hpp

src/boost/type_traits/remove_cv.hpp

src/boost/type_traits/is_signed.hpp

src/boost/type_traits/integral_constant.hpp

src/boost/type_traits/add_const.hpp

src/boost/type_traits/config.hpp

src/boost/type_traits/is_scalar.hpp

src/boost/type_traits/intrinsics.hpp

src/boost/type_traits/is_void.hpp

src/boost/type_traits/is_union.hpp

src/boost/type_traits/make_unsigned.hpp

src/boost/type_traits/is_lvalue_reference.hpp

src/boost/type_traits/is_member_pointer.hpp

src/boost/type_traits/remove_reference.hpp

src/boost/type_traits/is_float.hpp

src/boost/type_traits/add_volatile.hpp

src/boost/type_traits/is_class.hpp

src/boost/type_traits/add_reference.hpp

src/boost/type_traits/is_function.hpp

src/boost/type_traits/is_unsigned.hpp

src/boost/type_traits/is_volatile.hpp

src/boost/type_traits/is_rvalue_reference.hpp

src/boost/type_traits/is_integral.hpp

src/boost/type_traits/remove_bounds.hpp

src/boost/type_traits/add_lvalue_reference.hpp

src/boost/type_traits/is_arithmetic.hpp

src/boost/type_traits/broken_compiler_spec.hpp

src/boost/type_traits/is_reference.hpp

src/boost/type_traits/is_abstract.hpp

src/boost/type_traits/is_const.hpp

src/boost/type_traits/is_member_function_pointer.hpp

src/boost/type_traits/is_polymorphic.hpp

src/boost/type_traits/ice.hpp

src/boost/type_traits/is_same.hpp

src/boost/type_traits/is_array.hpp

src/boost/type_traits/is_convertible.hpp

src/boost/type_traits/is_enum.hpp

src/boost/type_traits/is_pointer.hpp

src/boost/type_traits/add_rvalue_reference.hpp

src/boost/type_traits/detail/ice_eq.hpp

src/boost/type_traits/detail/template_arity_spec.hpp

src/boost/type_traits/detail/yes_no_type.hpp

src/boost/type_traits/detail/ice_or.hpp

src/boost/type_traits/detail/ice_and.hpp

src/boost/type_traits/detail/cv_traits_impl.hpp

src/boost/type_traits/detail/type_trait_undef.hpp

src/boost/type_traits/detail/is_function_ptr_tester.hpp

src/boost/type_traits/detail/is_function_ptr_helper.hpp

src/boost/type_traits/detail/bool_trait_def.hpp

src/boost/type_traits/detail/type_trait_def.hpp

src/boost/type_traits/detail/is_mem_fun_pointer_impl.hpp

src/boost/type_traits/detail/wrap.hpp

src/boost/type_traits/detail/is_mem_fun_pointer_tester.hpp

src/boost/type_traits/detail/false_result.hpp

src/boost/type_traits/detail/bool_trait_undef.hpp

src/boost/type_traits/detail/ice_not.hpp

src/boost/type_traits/msvc/remove_cv.hpp

src/boost/type_traits/msvc/remove_reference.hpp

src/boost/type_traits/msvc/remove_bounds.hpp

src/boost/type_traits/msvc/typeof.hpp

src/boost/pending/integer_log2.hpp

src/boost/utility/enable_if.hpp

R/getGeneExpression_call.R R/getExpression.R R/getMeanVariance_call.R R/parseAlignment_call.R R/getDE.R R/estimateExpression_call.R R/methods.R R/tri_methods.R R/estimateDE_call.R R/estimateVBExpression_call.R R/getWithinGeneExpression_call.R R/estimateHyperPar_call.R

vignettes/BitSeq.Rnw

man/parseAlignment.Rd man/estimateVBExpression.Rd man/transcriptInfoFile.Rd man/BitSeq-package.Rd man/loadSamples.Rd man/estimateExpression.Rd man/transcriptInfo.Rd man/estimateHyperPar.Rd man/getMeanVariance.Rd man/estimateDE.Rd man/getDE.Rd man/getExpression.Rd man/getGeneExpression.Rd

inst/NEWS

inst/CITATION

inst/doc/BitSeq.Rnw

inst/doc/BitSeq.pdf inst/doc/BitSeq.R

inst/extdata/data-c1b1.rpkm

inst/extdata/data-c0b0.sam

inst/extdata/parameters1.txt

inst/extdata/ensSelect1.fasta

inst/extdata/data-c1b0.rpkm

inst/extdata/data-c0b1.rpkm

inst/extdata/ensSelect1.tr

BitSeq documentation built on Nov. 8, 2020, 5:25 p.m.