Files in LuyiTian/scPipe
pipeline for single cell RNA-seq data analysis

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/AllGenerics.R R/RcppExports.R R/SCE_methods.R R/biomart_methods.R R/get_read_str.R R/help.R R/qc.R R/sc_sample_data.R R/sc_sample_qc.R R/sc_workflow.R R/wrapper_scPipeCPP.R README.md
data/sc_sample_data.RData
data/sc_sample_qc.RData
inst/NEWS.Rd
inst/extdata/ERCC92.fa
inst/extdata/ERCC92_anno.gff3
inst/extdata/barcode_anno.csv
inst/extdata/report_template.Rmd inst/extdata/report_template_slim.Rmd
inst/extdata/simu_R1.fastq.gz
inst/extdata/simu_R2.fastq.gz
inst/scPipe.png
inst/workflow.png
man/QC_metrics.Rd man/UMI_dup_info.Rd man/UMI_duplication.Rd man/calculate_QC_metrics.Rd man/cell_barcode_matching.Rd man/convert_geneid.Rd man/create_processed_report.Rd man/create_report.Rd man/create_sce_by_dir.Rd man/demultiplex_info.Rd man/detect_outlier.Rd man/gene_id_type.Rd man/get_genes_by_GO.Rd man/organism.Rd man/plot_QC_pairs.Rd man/plot_UMI_dup.Rd man/plot_demultiplex.Rd man/plot_mapping.Rd man/remove_outliers.Rd man/scPipe.Rd man/sc_count_aligned_bam.Rd man/sc_demultiplex.Rd man/sc_demultiplex_and_count.Rd man/sc_detect_bc.Rd man/sc_exon_mapping.Rd man/sc_gene_counting.Rd man/sc_sample_data.Rd man/sc_sample_qc.Rd man/sc_trim_barcode.Rd
src/Eigen/Cholesky
src/Eigen/CholmodSupport
src/Eigen/Core
src/Eigen/Dense
src/Eigen/Eigen
src/Eigen/Eigenvalues
src/Eigen/Geometry
src/Eigen/Householder
src/Eigen/IterativeLinearSolvers
src/Eigen/Jacobi
src/Eigen/LU
src/Eigen/MetisSupport
src/Eigen/OrderingMethods
src/Eigen/PaStiXSupport
src/Eigen/PardisoSupport
src/Eigen/QR
src/Eigen/QtAlignedMalloc
src/Eigen/SPQRSupport
src/Eigen/SVD
src/Eigen/Sparse
src/Eigen/SparseCholesky
src/Eigen/SparseCore
src/Eigen/SparseLU
src/Eigen/SparseQR
src/Eigen/StdDeque
src/Eigen/StdList
src/Eigen/StdVector
src/Eigen/SuperLUSupport
src/Eigen/UmfPackSupport
src/Eigen/src/Cholesky/LDLT.h
src/Eigen/src/Cholesky/LLT.h
src/Eigen/src/Cholesky/LLT_LAPACKE.h
src/Eigen/src/CholmodSupport/CholmodSupport.h
src/Eigen/src/Core/Array.h
src/Eigen/src/Core/ArrayBase.h
src/Eigen/src/Core/ArrayWrapper.h
src/Eigen/src/Core/Assign.h
src/Eigen/src/Core/AssignEvaluator.h
src/Eigen/src/Core/Assign_MKL.h
src/Eigen/src/Core/BandMatrix.h
src/Eigen/src/Core/Block.h
src/Eigen/src/Core/BooleanRedux.h
src/Eigen/src/Core/CommaInitializer.h
src/Eigen/src/Core/ConditionEstimator.h
src/Eigen/src/Core/CoreEvaluators.h
src/Eigen/src/Core/CoreIterators.h
src/Eigen/src/Core/CwiseBinaryOp.h
src/Eigen/src/Core/CwiseNullaryOp.h
src/Eigen/src/Core/CwiseTernaryOp.h
src/Eigen/src/Core/CwiseUnaryOp.h
src/Eigen/src/Core/CwiseUnaryView.h
src/Eigen/src/Core/DenseBase.h
src/Eigen/src/Core/DenseCoeffsBase.h
src/Eigen/src/Core/DenseStorage.h
src/Eigen/src/Core/Diagonal.h
src/Eigen/src/Core/DiagonalMatrix.h
src/Eigen/src/Core/DiagonalProduct.h
src/Eigen/src/Core/Dot.h
src/Eigen/src/Core/EigenBase.h
src/Eigen/src/Core/ForceAlignedAccess.h
src/Eigen/src/Core/Fuzzy.h
src/Eigen/src/Core/GeneralProduct.h
src/Eigen/src/Core/GenericPacketMath.h
src/Eigen/src/Core/GlobalFunctions.h
src/Eigen/src/Core/IO.h
src/Eigen/src/Core/Inverse.h
src/Eigen/src/Core/Map.h
src/Eigen/src/Core/MapBase.h
src/Eigen/src/Core/MathFunctions.h
src/Eigen/src/Core/MathFunctionsImpl.h
src/Eigen/src/Core/Matrix.h
src/Eigen/src/Core/MatrixBase.h
src/Eigen/src/Core/NestByValue.h
src/Eigen/src/Core/NoAlias.h
src/Eigen/src/Core/NumTraits.h
src/Eigen/src/Core/PermutationMatrix.h
src/Eigen/src/Core/PlainObjectBase.h
src/Eigen/src/Core/Product.h
src/Eigen/src/Core/ProductEvaluators.h
src/Eigen/src/Core/Random.h
src/Eigen/src/Core/Redux.h
src/Eigen/src/Core/Ref.h
src/Eigen/src/Core/Replicate.h
src/Eigen/src/Core/ReturnByValue.h
src/Eigen/src/Core/Reverse.h
src/Eigen/src/Core/Select.h
src/Eigen/src/Core/SelfAdjointView.h
src/Eigen/src/Core/SelfCwiseBinaryOp.h
src/Eigen/src/Core/Solve.h
src/Eigen/src/Core/SolveTriangular.h
src/Eigen/src/Core/SolverBase.h
src/Eigen/src/Core/StableNorm.h
src/Eigen/src/Core/Stride.h
src/Eigen/src/Core/Swap.h
src/Eigen/src/Core/Transpose.h
src/Eigen/src/Core/Transpositions.h
src/Eigen/src/Core/TriangularMatrix.h
src/Eigen/src/Core/VectorBlock.h
src/Eigen/src/Core/VectorwiseOp.h
src/Eigen/src/Core/Visitor.h
src/Eigen/src/Core/arch/AVX/Complex.h
src/Eigen/src/Core/arch/AVX/MathFunctions.h
src/Eigen/src/Core/arch/AVX/PacketMath.h
src/Eigen/src/Core/arch/AVX/TypeCasting.h
src/Eigen/src/Core/arch/AVX512/MathFunctions.h
src/Eigen/src/Core/arch/AVX512/PacketMath.h
src/Eigen/src/Core/arch/AltiVec/Complex.h
src/Eigen/src/Core/arch/AltiVec/MathFunctions.h
src/Eigen/src/Core/arch/AltiVec/PacketMath.h
src/Eigen/src/Core/arch/CUDA/Complex.h
src/Eigen/src/Core/arch/CUDA/Half.h
src/Eigen/src/Core/arch/CUDA/MathFunctions.h
src/Eigen/src/Core/arch/CUDA/PacketMath.h
src/Eigen/src/Core/arch/CUDA/PacketMathHalf.h
src/Eigen/src/Core/arch/CUDA/TypeCasting.h
src/Eigen/src/Core/arch/Default/Settings.h
src/Eigen/src/Core/arch/NEON/Complex.h
src/Eigen/src/Core/arch/NEON/MathFunctions.h
src/Eigen/src/Core/arch/NEON/PacketMath.h
src/Eigen/src/Core/arch/SSE/Complex.h
src/Eigen/src/Core/arch/SSE/MathFunctions.h
src/Eigen/src/Core/arch/SSE/PacketMath.h
src/Eigen/src/Core/arch/SSE/TypeCasting.h
src/Eigen/src/Core/arch/ZVector/Complex.h
src/Eigen/src/Core/arch/ZVector/MathFunctions.h
src/Eigen/src/Core/arch/ZVector/PacketMath.h
src/Eigen/src/Core/functors/AssignmentFunctors.h
src/Eigen/src/Core/functors/BinaryFunctors.h
src/Eigen/src/Core/functors/NullaryFunctors.h
src/Eigen/src/Core/functors/StlFunctors.h
src/Eigen/src/Core/functors/TernaryFunctors.h
src/Eigen/src/Core/functors/UnaryFunctors.h
src/Eigen/src/Core/products/GeneralBlockPanelKernel.h
src/Eigen/src/Core/products/GeneralMatrixMatrix.h
src/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
src/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h
src/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h
src/Eigen/src/Core/products/GeneralMatrixVector.h
src/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h
src/Eigen/src/Core/products/Parallelizer.h
src/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
src/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h
src/Eigen/src/Core/products/SelfadjointMatrixVector.h
src/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h
src/Eigen/src/Core/products/SelfadjointProduct.h
src/Eigen/src/Core/products/SelfadjointRank2Update.h
src/Eigen/src/Core/products/TriangularMatrixMatrix.h
src/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h
src/Eigen/src/Core/products/TriangularMatrixVector.h
src/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h
src/Eigen/src/Core/products/TriangularSolverMatrix.h
src/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h
src/Eigen/src/Core/products/TriangularSolverVector.h
src/Eigen/src/Core/util/BlasUtil.h
src/Eigen/src/Core/util/Constants.h
src/Eigen/src/Core/util/DisableStupidWarnings.h
src/Eigen/src/Core/util/ForwardDeclarations.h
src/Eigen/src/Core/util/MKL_support.h
src/Eigen/src/Core/util/Macros.h
src/Eigen/src/Core/util/Memory.h
src/Eigen/src/Core/util/Meta.h
src/Eigen/src/Core/util/NonMPL2.h
src/Eigen/src/Core/util/ReenableStupidWarnings.h
src/Eigen/src/Core/util/StaticAssert.h
src/Eigen/src/Core/util/XprHelper.h
src/Eigen/src/Eigenvalues/ComplexEigenSolver.h
src/Eigen/src/Eigenvalues/ComplexSchur.h
src/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h
src/Eigen/src/Eigenvalues/EigenSolver.h
src/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h
src/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
src/Eigen/src/Eigenvalues/HessenbergDecomposition.h
src/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
src/Eigen/src/Eigenvalues/RealQZ.h
src/Eigen/src/Eigenvalues/RealSchur.h
src/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h
src/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
src/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h
src/Eigen/src/Eigenvalues/Tridiagonalization.h
src/Eigen/src/Geometry/AlignedBox.h
src/Eigen/src/Geometry/AngleAxis.h
src/Eigen/src/Geometry/EulerAngles.h
src/Eigen/src/Geometry/Homogeneous.h
src/Eigen/src/Geometry/Hyperplane.h
src/Eigen/src/Geometry/OrthoMethods.h
src/Eigen/src/Geometry/ParametrizedLine.h
src/Eigen/src/Geometry/Quaternion.h
src/Eigen/src/Geometry/Rotation2D.h
src/Eigen/src/Geometry/RotationBase.h
src/Eigen/src/Geometry/Scaling.h
src/Eigen/src/Geometry/Transform.h
src/Eigen/src/Geometry/Translation.h
src/Eigen/src/Geometry/Umeyama.h
src/Eigen/src/Geometry/arch/Geometry_SSE.h
src/Eigen/src/Householder/BlockHouseholder.h
src/Eigen/src/Householder/Householder.h
src/Eigen/src/Householder/HouseholderSequence.h
src/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
src/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
src/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
src/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h
src/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
src/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
src/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h
src/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h
src/Eigen/src/Jacobi/Jacobi.h
src/Eigen/src/LU/Determinant.h
src/Eigen/src/LU/FullPivLU.h
src/Eigen/src/LU/InverseImpl.h
src/Eigen/src/LU/PartialPivLU.h
src/Eigen/src/LU/PartialPivLU_LAPACKE.h
src/Eigen/src/LU/arch/Inverse_SSE.h
src/Eigen/src/MetisSupport/MetisSupport.h
src/Eigen/src/OrderingMethods/Amd.h
src/Eigen/src/OrderingMethods/Eigen_Colamd.h
src/Eigen/src/OrderingMethods/Ordering.h
src/Eigen/src/PaStiXSupport/PaStiXSupport.h
src/Eigen/src/PardisoSupport/PardisoSupport.h
src/Eigen/src/QR/ColPivHouseholderQR.h
src/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h
src/Eigen/src/QR/CompleteOrthogonalDecomposition.h
src/Eigen/src/QR/FullPivHouseholderQR.h
src/Eigen/src/QR/HouseholderQR.h
src/Eigen/src/QR/HouseholderQR_LAPACKE.h
src/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
src/Eigen/src/SVD/BDCSVD.h
src/Eigen/src/SVD/JacobiSVD.h
src/Eigen/src/SVD/JacobiSVD_LAPACKE.h
src/Eigen/src/SVD/SVDBase.h
src/Eigen/src/SVD/UpperBidiagonalization.h
src/Eigen/src/SparseCholesky/SimplicialCholesky.h
src/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h
src/Eigen/src/SparseCore/AmbiVector.h
src/Eigen/src/SparseCore/CompressedStorage.h
src/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
src/Eigen/src/SparseCore/MappedSparseMatrix.h
src/Eigen/src/SparseCore/SparseAssign.h
src/Eigen/src/SparseCore/SparseBlock.h
src/Eigen/src/SparseCore/SparseColEtree.h
src/Eigen/src/SparseCore/SparseCompressedBase.h
src/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
src/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
src/Eigen/src/SparseCore/SparseDenseProduct.h
src/Eigen/src/SparseCore/SparseDiagonalProduct.h
src/Eigen/src/SparseCore/SparseDot.h
src/Eigen/src/SparseCore/SparseFuzzy.h
src/Eigen/src/SparseCore/SparseMap.h
src/Eigen/src/SparseCore/SparseMatrix.h
src/Eigen/src/SparseCore/SparseMatrixBase.h
src/Eigen/src/SparseCore/SparsePermutation.h
src/Eigen/src/SparseCore/SparseProduct.h
src/Eigen/src/SparseCore/SparseRedux.h
src/Eigen/src/SparseCore/SparseRef.h
src/Eigen/src/SparseCore/SparseSelfAdjointView.h
src/Eigen/src/SparseCore/SparseSolverBase.h
src/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
src/Eigen/src/SparseCore/SparseTranspose.h
src/Eigen/src/SparseCore/SparseTriangularView.h
src/Eigen/src/SparseCore/SparseUtil.h
src/Eigen/src/SparseCore/SparseVector.h
src/Eigen/src/SparseCore/SparseView.h
src/Eigen/src/SparseCore/TriangularSolver.h
src/Eigen/src/SparseLU/SparseLU.h
src/Eigen/src/SparseLU/SparseLUImpl.h
src/Eigen/src/SparseLU/SparseLU_Memory.h
src/Eigen/src/SparseLU/SparseLU_Structs.h
src/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
src/Eigen/src/SparseLU/SparseLU_Utils.h
src/Eigen/src/SparseLU/SparseLU_column_bmod.h
src/Eigen/src/SparseLU/SparseLU_column_dfs.h
src/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
src/Eigen/src/SparseLU/SparseLU_gemm_kernel.h
src/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
src/Eigen/src/SparseLU/SparseLU_kernel_bmod.h
src/Eigen/src/SparseLU/SparseLU_panel_bmod.h
src/Eigen/src/SparseLU/SparseLU_panel_dfs.h
src/Eigen/src/SparseLU/SparseLU_pivotL.h
src/Eigen/src/SparseLU/SparseLU_pruneL.h
src/Eigen/src/SparseLU/SparseLU_relax_snode.h
src/Eigen/src/SparseQR/SparseQR.h
src/Eigen/src/StlSupport/StdDeque.h
src/Eigen/src/StlSupport/StdList.h
src/Eigen/src/StlSupport/StdVector.h
src/Eigen/src/StlSupport/details.h
src/Eigen/src/SuperLUSupport/SuperLUSupport.h
src/Eigen/src/UmfPackSupport/UmfPackSupport.h
src/Eigen/src/misc/Image.h
src/Eigen/src/misc/Kernel.h
src/Eigen/src/misc/RealSvd2x2.h
src/Eigen/src/misc/blas.h
src/Eigen/src/misc/lapack.h
src/Eigen/src/misc/lapacke.h
src/Eigen/src/misc/lapacke_mangling.h
src/Eigen/src/plugins/ArrayCwiseBinaryOps.h
src/Eigen/src/plugins/ArrayCwiseUnaryOps.h
src/Eigen/src/plugins/BlockMethods.h
src/Eigen/src/plugins/CommonCwiseBinaryOps.h
src/Eigen/src/plugins/CommonCwiseUnaryOps.h
src/Eigen/src/plugins/MatrixCwiseBinaryOps.h
src/Eigen/src/plugins/MatrixCwiseUnaryOps.h
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/cellbarcode.cpp
src/cellbarcode.h
src/config_hts.h
src/detect_barcode.cpp
src/detect_barcode.h
src/global_config.h
src/parsebam.cpp
src/parsebam.h
src/parsecount.cpp
src/parsecount.h
src/rcpp_scPipe_func.cpp
src/transcriptmapping.cpp
src/transcriptmapping.h
src/trimbarcode.cpp
src/trimbarcode.h
src/utils.cpp
src/utils.h
tests/testthat.R tests/testthat/test_sce.R vignettes/scPipe_tutorial.Rmd
LuyiTian/scPipe documentation built on Dec. 22, 2017, 6:50 a.m.