├── .DS_Store ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── .Rapp.history ├── MultiCCA.R ├── architectures.R ├── backend_decoder.R ├── backend_encoder.R ├── data.R ├── scAlign.R ├── scAlignClass.R ├── scAlignMulti.R ├── scAlignSeuratWrapper.R ├── train_decoder.R ├── train_encoder.R ├── train_encoder_multi.R └── utils.R ├── README.md ├── data ├── .DS_Store └── cellbench.rda ├── man ├── DecoderVariance.Rd ├── ExtractGenes.Rd ├── GetCharMetadata.Rd ├── GetCrit.Rd ├── MeanDecoderVariance.Rd ├── PlotTSNE.Rd ├── RunMultiCCA.Rd ├── SelectColors.Rd ├── UpdateW.Rd ├── alignment_score.Rd ├── as.SingleCellExperimentList.Rd ├── cellbench.Rd ├── compute_kernel_matrix.Rd ├── decoderModel_add_mse_loss.Rd ├── decoderModel_calc_projection.Rd ├── decoderModel_create_train_op.Rd ├── decoderModel_emb_to_proj.Rd ├── decoderModel_train_decoder.Rd ├── decoder_large.Rd ├── decoder_medium.Rd ├── decoder_small.Rd ├── define_kernel_matrix.Rd ├── dot-check_all_args.Rd ├── dot-check_tensorflow.Rd ├── dot-data_setup.Rd ├── dot-early_stop.Rd ├── dot-is.wholenumber.Rd ├── dot-learning_rate.Rd ├── dot-plotTSNE.Rd ├── encoderModel_add_logit_loss.Rd ├── encoderModel_add_semisup_loss_data_driven.Rd ├── encoderModel_calc_embedding.Rd ├── encoderModel_calc_logit.Rd ├── encoderModel_create_train_op.Rd ├── encoderModel_data_to_embedding.Rd ├── encoderModel_embedding_to_logit.Rd ├── encoderModel_gaussian_kernel.Rd ├── encoderModel_train_encoder.Rd ├── encoderModel_train_encoder_multi.Rd ├── encoder_large.Rd ├── encoder_medium.Rd ├── encoder_small.Rd ├── gaussianKernel.Rd ├── l2n.Rd ├── scAlign.Rd ├── scAlignArguments.Rd ├── scAlignCreateObject.Rd ├── scAlignMulti.Rd └── scAlignOptions.Rd └── tests ├── testthat.R └── testthat └── test-scalign.R /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/scAlign/HEAD/.DS_Store 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