List of all items
Structs
- beadcountweights::BeadCountWeights
- bwss::Bwss
- cumoverlap::CumOverlap
- decidetests::TestResults
- decidetests::TestResultsSummary
- diffsplice::DiffSplice
- diffsplice::TopSpliceRow
- dups::DupCorOutput
- fit::MArrayLM
- fitmixture::FitMixture
- genas::Genas
- geneset::CameraResult
- geneset::ContrastAsCoef
- geneset::FryResult
- geneset::MroastRow
- geneset::Roast
- geneset::RomerRow
- io::LabeledMatrix
- io::WriteFitOptions
- lowess::LoessFit
- lowess::WeightedLowess
- modelmatrix::ModelMatrix
- normexp::NormexpFit
- normwithin::PrinterLayout
- optim::NelderMead
- poolvar::PoolVar
- rng::RRng
- selectmodel::SelectModelResult
- toptable::TopRow
- toptable::TopRowF
- voom::VoomOutput
- voom::VoomQualityWeights
- voom::VoomaByGroupOutput
- voom::VoomaLmFit
- voom::VoomaOutput
Enums
- beadcountweights::BeadDispersion
- decidetests::Adjust
- decidetests::DecideMethod
- diffsplice::SpliceSort
- diffsplice::SpliceTest
- genas::GenasSubset
- geneset::Alternative
- geneset::Direction
- geneset::FrySort
- geneset::RomerAlternative
- geneset::RomerStatistic
- ma3x3::Ma3x3Fun
- modelmatrix::ModelParam
- norm::CyclicMethod
- norm::NormalizeMethod
- normexp::BackgroundMethod
- normwithin::WithinArrayMethod
- proptruenull::PropTrueNullMethod
- selectmodel::SelectCriterion
- toptable::SortBy
- zscore::ZscoreTMethod
Functions
- arrayweights::array_weights
- arrayweights::array_weights_gene_by_gene
- arrayweights::array_weights_prwts_reml
- arrayweights::array_weights_quick
- auroc::auroc
- avereps::avearrays
- avereps::avereps
- batch::remove_batch_effect
- beadcountweights::bead_count_weights
- bwss::bwss
- bwss::bwss_matrix
- classifytestsf::classify_tests_f
- classifytestsf::classify_tests_fstat
- combine::make_unique
- contrasts::contrasts_fit
- contrasts::make_contrasts
- cumoverlap::cum_overlap
- decidetests::classify_tests_p
- decidetests::decide_tests
- decidetests::decide_tests_pvalues
- decidetests::p_adjust
- detectionpvalues::detection_p_values
- diffsplice::diff_splice
- diffsplice::top_splice
- dups::avedups
- dups::duplicate_correlation
- dups::uniquegenelist
- dups::unwrapdups
- ebayes::ebayes
- fit::is_fullrank
- fit::lmfit
- fit::lmfit_weighted
- fit::non_estimable
- fitgamma::fit_gamma_intercept
- fitmixture::fitmixture
- genas::genas
- geneset::camera
- geneset::camera_pr
- geneset::contrast_as_coef
- geneset::fry
- geneset::gene_set_test
- geneset::ids2indices
- geneset::inter_gene_correlation
- geneset::mroast
- geneset::rank_sum_test_with_correlation
- geneset::roast
- geneset::romer
- geneset::top_romer
- geneset::wilcox_gst
- glsseries::gls_series
- io::align_contrasts
- io::align_design
- io::read_matrix
- io::read_matrix_with_delimiter
- io::write_fit
- io::write_fit_dump
- io::write_test_results
- io::write_top_table
- io::write_top_table_f
- linalg::block_diag
- linalg::cholesky_upper
- linalg::cov2cor
- linalg::eigh
- linalg::inv_upper
- linalg::matrix_rank
- linalg::qr_econ
- linalg::qr_full_q
- linalg::solve_upper
- linalg::solve_upper_transpose
- linalg::svd_left
- linalg::xtx_inv_from_r
- logsumexp::logcosh
- logsumexp::logsumexp
- lowess::loess_fit
- lowess::weighted_lowess
- ma3x3::ma3x3_matrix
- ma3x3::ma3x3_spottedarray
- modelmatrix::model_matrix
- modelmatrix::unique_targets
- mrlm::mrlm
- neqc::nec
- neqc::neqc
- neqc::normexp_fit_control
- neqc::normexp_fit_detection_p
- norm::normalize_between_arrays
- norm::normalize_cyclic_loess
- norm::normalize_median_abs_values
- norm::normalize_median_values
- norm::normalize_quantiles
- normexp::background_correct_matrix
- normexp::normexp_fit_saddle
- normexp::normexp_signal
- normwithin::ma_from_rg
- normwithin::normalize_within_arrays
- normwithin::rg_from_ma
- optim::nelder_mead
- optim::nelder_mead_with
- poolvar::pool_var
- predfcm::pred_fcm
- printtipweights::printtip_weights
- propexpr::propexpr
- proptruenull::convest
- proptruenull::prop_true_null
- qqt::qqf
- qqt::qqt
- rng::qnorm
- selectmodel::select_model
- sepchannel::design_i2a
- sepchannel::design_i2m
- sepchannel::exprs_ma
- sepchannel::lmsc_fit
- special::betai
- special::chi2_sf
- special::chisq_pdf
- special::chisq_qf
- special::digamma
- special::f_lsf
- special::f_pdf
- special::f_qf
- special::f_sf
- special::gauss_legendre_01
- special::ln_beta
- special::ln_betai
- special::ln_gamma
- special::ln_gamma_lr
- special::ln_gamma_ur
- special::logmdigamma
- special::t_isf
- special::t_ppf
- special::t_sf
- special::t_two_sided_pvalue
- special::tetragamma
- special::trigamma
- special::trigamma_inverse
- toptable::p_adjust_bh
- toptable::top_table
- toptable::top_table_f
- toptable::top_treat
- treat::treat
- tricube::tricube_moving_average
- voom::choose_lowess_span
- voom::voom
- voom::voom_with_quality_weights
- voom::vooma
- voom::vooma_by_group
- voom::vooma_lm_fit
- weightedmedian::weighted_median
- weights::as_matrix_weights
- weights::modify_weights
- wsva::wsva
- zscore::t_zscore
- zscore::zscore_from_log_tails
- zscore::zscore_gamma
- zscore::zscore_t
- zscorehyper::zscore_hyper