Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | Z _ _col_order (abaco.batch_correction.ConQur attribute) _feature_cols (abaco.batch_correction.ConQur attribute) _logit_models (abaco.batch_correction.ConQur attribute) _quantile_models (abaco.batch_correction.ConQur attribute) A a_ (abaco.batch_correction.PLSDA attribute) abaco module abaco.ABaCo module abaco.batch_correction module abaco.dataloader module abaco.metrics module abaco.plots module abaco.utils module abaco_recon() (in module abaco.ABaCo) abaco_recon_ensemble() (in module abaco.ABaCo) abaco_run() (in module abaco.ABaCo) abaco_run_ensemble() (in module abaco.ABaCo) ABaCoDataLoader() (in module abaco.dataloader) adversarial_loss() (in module abaco.ABaCo) all_metrics() (in module abaco.metrics) arg_constraints (abaco.ABaCo.DirichletMultinomial attribute) (abaco.ABaCo.MixtureOfGaussians attribute) (abaco.ABaCo.ZIDM attribute) (abaco.ABaCo.ZINB attribute) ARI() (in module abaco.metrics) assert_nonempty_keys() (in module abaco.utils) assert_nonempty_vals() (in module abaco.utils) assert_path() (in module abaco.utils) ASW() (in module abaco.metrics) B b_ (abaco.batch_correction.PLSDA attribute) batch_correct() (abaco.ABaCo.metaABaCo method) batch_mask() (abaco.ABaCo.metaABaCo method) BatchDiscriminator (class in abaco.ABaCo) C class_to_int() (in module abaco.dataloader) cLISI_full_rank() (in module abaco.metrics) cLISI_norm() (in module abaco.metrics) cLISI_raw() (in module abaco.metrics) cluster_loss() (abaco.ABaCo.MoCPPrior method) (abaco.ABaCo.VMMPrior method) ConditionalEnsembleVAE (class in abaco.ABaCo) ConditionalVAE (class in abaco.ABaCo) ConQur (class in abaco.batch_correction) contour_plot() (in module abaco.ABaCo) correct() (abaco.ABaCo.metaABaCo method) correctBMC() (in module abaco.batch_correction) correctCombat() (in module abaco.batch_correction) correctCombatSeq() (in module abaco.batch_correction) correctConQuR() (in module abaco.batch_correction) correctLimma_rBE() (in module abaco.batch_correction) correctPLSDAbatch() (in module abaco.batch_correction) correctPLSDAbatch_R() (in module abaco.batch_correction) create_folder() (in module abaco.utils) D DataPreprocess() (in module abaco.dataloader) DataReverseTransform() (in module abaco.dataloader) DataTransform() (in module abaco.dataloader) decode() (abaco.ABaCo.VAE method) deflate_mtx() (in module abaco.batch_correction) det_encode() (abaco.ABaCo.MoGEncoder method) (abaco.ABaCo.NormalEncoder method) df_joiner() (in module abaco.utils) DirichletMultinomial (class in abaco.ABaCo) DMDecoder (class in abaco.ABaCo) E elbo() (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) encode() (abaco.ABaCo.MoCPEncoder method) (abaco.ABaCo.MoGEncoder method) (abaco.ABaCo.NormalEncoder method) (abaco.ABaCo.VAE method) entropy() (abaco.ABaCo.MixtureOfGaussians method) exp_var_ (abaco.batch_correction.PLSDA attribute) F fit() (abaco.ABaCo.metaABaCo method) (abaco.batch_correction.ConQur method) (abaco.batch_correction.PLSDA method) forward() (abaco.ABaCo.BatchDiscriminator method) (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) (abaco.ABaCo.DMDecoder method) (abaco.ABaCo.MoCPEncoder method) (abaco.ABaCo.MoCPPrior method) (abaco.ABaCo.MoGEncoder method) (abaco.ABaCo.MoGPrior method) (abaco.ABaCo.NBDecoder method) (abaco.ABaCo.NormalEncoder method) (abaco.ABaCo.NormalPrior method) (abaco.ABaCo.SupervisedContrastiveLoss method) (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) (abaco.ABaCo.VMMPrior method) (abaco.ABaCo.ZIDMDecoder method) (abaco.ABaCo.ZINBDecoder method) G generate_log_filename() (in module abaco.utils) get_args() (in module abaco.utils) get_basename() (in module abaco.utils) get_logger() (in module abaco.utils) get_posterior() (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) (abaco.ABaCo.VAE method) (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) get_prior() (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) get_time() (in module abaco.utils) H has_rsample (abaco.ABaCo.DirichletMultinomial attribute) (abaco.ABaCo.MixtureOfGaussians attribute) (abaco.ABaCo.ZIDM attribute) (abaco.ABaCo.ZINB attribute) I iLISI_full_rank() (in module abaco.metrics) iLISI_norm() (in module abaco.metrics) iLISI_raw() (in module abaco.metrics) init_log() (in module abaco.utils) iters_ (abaco.batch_correction.PLSDA attribute) K kBET() (in module abaco.metrics) kl_div_loss() (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) kl_divergence() (abaco.ABaCo.VAE method) kl_mog_mog() (in module abaco.ABaCo) kl_zinb_zinb() (in module abaco.ABaCo) L log_normal_diag() (in module abaco.ABaCo) log_prob() (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) (abaco.ABaCo.DirichletMultinomial method) (abaco.ABaCo.MixtureOfGaussians method) (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) (abaco.ABaCo.ZIDM method) (abaco.ABaCo.ZINB method) loss() (abaco.ABaCo.BatchDiscriminator method) M mean (abaco.ABaCo.MixtureOfGaussians property) metaABaCo (class in abaco.ABaCo) MixtureOfGaussians (class in abaco.ABaCo) MoCPEncoder (class in abaco.ABaCo) MoCPPrior (class in abaco.ABaCo) module abaco abaco.ABaCo abaco.batch_correction abaco.dataloader abaco.metrics abaco.plots abaco.utils MoGEncoder (class in abaco.ABaCo) MoGPrior (class in abaco.ABaCo) monte_carlo_encode() (abaco.ABaCo.MoGEncoder method) (abaco.ABaCo.NormalEncoder method) N NBDecoder (class in abaco.ABaCo) new_pre_train_abaco() (in module abaco.ABaCo) NMI() (in module abaco.metrics) NormalEncoder (class in abaco.ABaCo) normalize_url() (in module abaco.utils) NormalPrior (class in abaco.ABaCo) O one_hot_encoding() (in module abaco.dataloader) P pairwise_distance() (in module abaco.metrics) pairwise_distance_multi_run() (in module abaco.metrics) pairwise_distance_std() (in module abaco.metrics) pca_posterior() (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) (abaco.ABaCo.VAE method) (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) pca_prior() (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) PERMANOVA() (in module abaco.metrics) plot_LISI_perplexity() (in module abaco.plots) plot_pca_posterior() (abaco.ABaCo.metaABaCo method) plotClusterHeatMap() (in module abaco.plots) plotOTUBox() (in module abaco.plots) plotPCA() (in module abaco.plots) plotPCoA() (in module abaco.plots) plotRLE() (in module abaco.plots) PLSDA (class in abaco.batch_correction) pre_train_abaco() (in module abaco.ABaCo) pre_train_abaco_ensemble() (in module abaco.ABaCo) R rsample() (abaco.ABaCo.MixtureOfGaussians method) S sample() (abaco.ABaCo.ConditionalEnsembleVAE method) (abaco.ABaCo.ConditionalVAE method) (abaco.ABaCo.DirichletMultinomial method) (abaco.ABaCo.MixtureOfGaussians method) (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) (abaco.ABaCo.ZIDM method) (abaco.ABaCo.ZINB method) sample_from_dataloader() (abaco.ABaCo.VampPriorMixtureConditionalEnsembleVAE method) (abaco.ABaCo.VampPriorMixtureConditionalVAE method) (abaco.ABaCo.VMMPrior method) set_fit_request() (abaco.batch_correction.ConQur method) set_transform_request() (abaco.batch_correction.ConQur method) SupervisedContrastiveLoss (class in abaco.ABaCo) support (abaco.ABaCo.DirichletMultinomial attribute) (abaco.ABaCo.MixtureOfGaussians attribute) (abaco.ABaCo.ZIDM attribute) (abaco.ABaCo.ZINB attribute) T t_ (abaco.batch_correction.PLSDA attribute) train_abaco() (in module abaco.ABaCo) train_abaco_ensemble() (in module abaco.ABaCo) train_vae() (abaco.ABaCo.metaABaCo method) transform() (abaco.batch_correction.ConQur method) U u_ (abaco.batch_correction.PLSDA attribute) V VAE (class in abaco.ABaCo) VampPriorMixtureConditionalEnsembleVAE (class in abaco.ABaCo) VampPriorMixtureConditionalVAE (class in abaco.ABaCo) variance() (abaco.ABaCo.MixtureOfGaussians method) VMMPrior (class in abaco.ABaCo) Z ZIDM (class in abaco.ABaCo) ZIDMDecoder (class in abaco.ABaCo) ZINB (class in abaco.ABaCo) ZINBDecoder (class in abaco.ABaCo)
