List of all items

Structs

• core::dgelist::DgeList
• core::filtering::FilterParams
• core::normalisation::NormParams
• dispersion::apl::AplWorkspace
• dispersion::cox_reid::CoxReidParams
• dispersion::estimate::DispersionEstimates
• dispersion::estimate::EstimateDispParams
• dispersion::estimate::WlebParams
• dispersion::estimate::WlebResult
• exact::ExactTestParams
• exact::ExactTestResult
• glm::fit::GlmFit
• glm::levenberg::LevenbergFit
• glm::levenberg::LevenbergParams
• glm::levenberg::Scratch
• glm::one_group::OneGroupParams
• glm::one_way::OneWayFit
• glm::ql_fit::QlFit
• glm::ql_fit::QlFitParams
• glm::test::GlmTest
• glm::test::GlmTestInput
• glm::test::QlSummary
• limma::array_weights::ArrayWeightParams
• limma::ebayes::EBayesParams
• limma::lm_fit::LmFitResult
• limma::lowess::LowessFit
• limma::lowess::LowessParams
• limma::marray::MArrayLm
• limma::scran_lowess::ScranLowessParams
• limma::smoothing::LoessFit
• limma::squeeze_var::SqueezeVarParams
• limma::squeeze_var::SqueezeVarResult
• limma::squeeze_var::UnequalDf1Fit
• limma::toptable::TopTable
• limma::toptable::TopTableF
• limma::toptable::TopTableParams
• limma::voom::VoomParams
• limma::voom::VoomResult
• numeric::bobyqa::BobyqaParams
• numeric::bobyqa::BobyqaResult
• numeric::bobyqa::BobyqaStepper
• numeric::interpolate::FmmSpline
• numeric::lbfgsb::LbfgsbParams
• numeric::lbfgsb::LbfgsbResult
• numeric::optimise::NelderMeadParams
• numeric::optimise::NelderMeadResult
• numeric::optimise::NelderMeadStepper
• ql::weights::AdjustedDeviance
• results::TopTags
• sc::nebula::NebulaFit
• sc::nebula::NebulaParams
• sc::pml::PmlData
• sc::pml::PmlObjective
• sc::pml::PmlParams
• sc::pml::PmlResult
• sc::pml::PmlVariance
• sc::ptmg::GeneCounts
• sc::ptmg::GeneData
• sc::ptmg::OffsetSummary
• sc::shrink::ShrinkParams
• sc::shrink::ShrinkResult
• sc::test::ScTestResult
• splicing::DiffSpliceParams
• splicing::DiffSpliceQl
• splicing::DiffSpliceResult
• utils::design::ContrastDesign
• utils::sparse::CompressedSparse

Enums

• core::dgelist::DispersionKind
• core::normalisation::NormMethod
• dispersion::estimate::TrendMethod
• errors::EdgeErrors
• exact::RejectionRegion
• glm::fit::FitMethod
• glm::levenberg::StartMethod
• glm::test::Tested
• glm::test::TreatNull
• limma::array_weights::ArrayWeightMethod
• limma::ebayes::EBayesTrend
• limma::toptable::TopTableResort
• limma::toptable::TopTableSort
• numeric::bobyqa::BobyqaStatus
• numeric::lbfgsb::LbfgsbStatus
• results::SortBy
• sc::nebula::NebulaMethod
• sc::test::ScTested
• utils::recycled::Recycled
• utils::recycled::RecycledRow
• utils::simd::SimdLevel
• utils::sparse::SparseFormat

Traits

• utils::simd::EdgeSimd
• utils::traits::EdgeFloat

Functions

• core::expression::ave_log_cpm
• core::expression::cpm
• core::expression::rpkm
• core::expression::tpm
• core::filtering::filter_by_expr
• core::normalisation::calc_norm_factors
• core::normalisation::parse_norm_method
• dispersion::apl::apl_at
• dispersion::apl::apl_grid
• dispersion::cox_reid::common_dispersion_cox_reid
• dispersion::cox_reid::systematic_subset
• dispersion::estimate::estimate_disp
• dispersion::estimate::parse_trend_method
• dispersion::estimate::residual_df
• dispersion::estimate::wleb
• exact::equalize_lib_sizes
• exact::exact_test
• exact::q2q_nbinom
• glm::deviance::unit_nb_deviance
• glm::fit::add_prior_count
• glm::fit::glm_fit
• glm::fit::glm_fit_dge
• glm::levenberg::mglm_levenberg
• glm::one_group::mglm_one_group
• glm::one_way::mglm_one_way
• glm::ql_fit::glm_ql_fit
• glm::test::glm_lrt
• glm::test::glm_ql_ftest
• glm::test::glm_treat
• limma::array_weights::array_weights
• limma::array_weights::duplicate_correlation
• limma::contrasts::contrasts_fit
• limma::contrasts::make_contrasts
• limma::ebayes::ebayes
• limma::lm_fit::lm_fit
• limma::lowess::lowess
• limma::lowess::weighted_lowess
• limma::remove_batch_effect::remove_batch_effect
• limma::scran_lowess::scran_lowess
• limma::smoothing::locfit_by_col
• limma::smoothing::loess_by_col
• limma::squeeze_var::fit_f_dist
• limma::squeeze_var::fit_f_dist_robustly
• limma::squeeze_var::fit_f_dist_trend
• limma::squeeze_var::fit_f_dist_unequal_df1
• limma::squeeze_var::squeeze_var
• limma::toptable::top_table
• limma::toptable::top_table_f
• limma::voom::voom
• limma::voom::voom_basic
• limma::voom::voom_lmfit
• numeric::bobyqa::bobyqa
• numeric::dist::beta_cdf
• numeric::dist::beta_ppf
• numeric::dist::beta_sf
• numeric::dist::chisq_sf
• numeric::dist::f_ppf
• numeric::dist::f_sf
• numeric::dist::gamma_cdf
• numeric::dist::gamma_ppf
• numeric::dist::nbinom_cdf
• numeric::dist::nbinom_ln_pmf
• numeric::dist::norm_cdf
• numeric::dist::norm_ppf
• numeric::dist::norm_sf
• numeric::dist::t_cdf
• numeric::dist::t_isf_log
• numeric::dist::t_ppf
• numeric::dist::t_sf
• numeric::dist::t_sf_log
• numeric::gamma::digamma
• numeric::gamma::ln_gamma
• numeric::gamma::logmdigamma
• numeric::gamma::polygamma
• numeric::gamma::trigamma
• numeric::gamma::trigamma_inverse
• numeric::interpolate::fmm_spline
• numeric::interpolate::interp_linear_extrap
• numeric::interpolate::maximize_interpolant
• numeric::interpolate::maximize_interpolant_many
• numeric::interpolate::natural_spline_basis
• numeric::lbfgsb::minimise
• numeric::optimise::brent_fmin
• numeric::optimise::brentq
• numeric::optimise::nelder_mead
• numeric::stats::median
• numeric::stats::moving_average_by_col
• numeric::stats::p_adjust_bh
• numeric::stats::quantile_type7
• numeric::stats::rank_average
• numeric::stats::trimmed_mean
• ql::chebyshev::cheb_eval
• ql::chebyshev::cheb_eval_2d
• ql::chebyshev::compute_weight
• ql::chebyshev::nb_alpha
• ql::chebyshev::nb_kappa
• ql::chebyshev::pois_alpha
• ql::chebyshev::pois_kappa
• ql::weights::compute_adjust_vec
• ql::weights::compute_prior
• ql::weights::update_prior
• results::decide_tests
• results::top_tags
• sc::nebula::nebula
• sc::nebula::nebula_sparse
• sc::pml::check_convergence
• sc::pml::opt_pml
• sc::pml::opt_pml_nbm
• sc::pml::pml_log_likelihood_gradient
• sc::ptmg::cell_level_columns
• sc::ptmg::centre_design
• sc::ptmg::cumsum_y
• sc::ptmg::design_cv
• sc::ptmg::offset_summary
• sc::ptmg::positive_indices
• sc::ptmg::ptmg_gradient
• sc::ptmg::ptmg_neg_log_likelihood
• sc::ptmg::ptmg_value_and_gradient
• sc::ptmg::ptmg_value_gradient_hessian
• sc::shrink::sc_residual_df
• sc::shrink::shrink_sc_dispersion
• sc::test::glm_sc_test
• sc::test::packed_len
• splicing::diff_splice
• splicing::diff_splice_dge
• splicing::splice_variants
• utils::design::choose_lowess_span
• utils::design::contrast_as_coef
• utils::design::design_as_factor
• utils::design::hat_diagonal
• utils::design::is_full_rank
• utils::design::matrix_rank
• utils::design::non_estimable
• utils::simd::detect_simd_level

Constants

• exact::BIG_COUNT_DEFAULT
• exact::PRIOR_COUNT_DEFAULT
• glm::deviance::GAMMA_REGIME
• glm::deviance::MILDLY_LOW_VALUE
• glm::deviance::POISSON_REGIME
• glm::fit::DEFAULT_PRIOR_COUNT
• limma::toptable::DEFAULT_CONF_LEVEL
• numeric::optimise::OPTIMIZE_TOL
• sc::nebula::CONV_OUTER_FAILED
• sc::pml::CONV_AT_BOUND
• sc::pml::CONV_CRITICAL_POINT
• sc::pml::CONV_MAX_ITER
• sc::pml::CONV_NOT_FINITE
• sc::pml::CONV_SINGULAR
• sc::pml::CONV_STALLED
• sc::pml::CONV_SUCCESS
• utils::design::LIMMA_LOWESS_DEFAULTS