Man pages for quon-titative-biology/scAlign
An alignment and integration method for single cell genomics
| alignment_score | Computes alignment score |
| as.SingleCellExperimentList | Converts a list of Seurat objects into a list of Single Cell... |
| cellbench | CellBench data for benchmarking |
| compute_kernel_matrix | Computes kernel matrix |
| decoder_large | Network large |
| decoder_medium | Network medium |
| decoderModel_add_mse_loss | Convert embedding to logit scores |
| decoderModel_calc_projection | Compute projections for complete data after training |
| decoderModel_create_train_op | Builds training operation |
| decoderModel_emb_to_proj | Compute projection for mini-batch |
| decoderModel_train_decoder | decoder for scAlign |
| decoder_small | Network small |
| DecoderVariance | Creates a 2d array of variance values calculated across the... |
| define_kernel_matrix | define kernel matrix |
| dot-check_all_args | Check arguments |
| dot-check_tensorflow | Check tf install |
| dot-data_setup | Sets data |
| dot-early_stop | Perform early stopping |
| dot-is.wholenumber | Check for whole number |
| dot-learning_rate | Sets the learning rate for optimizer |
| dot-plotTSNE | Creates tsne plot |
| encoder_large | Network large |
| encoder_medium | Network medium |
| encoderModel_add_logit_loss | Add classifier loss component |
| encoderModel_add_semisup_loss_data_driven | Add walker loss component |
| encoderModel_calc_embedding | Compute embedding for complete data after training |
| encoderModel_calc_logit | Compute embedding for complete data after training |
| encoderModel_create_train_op | Builds training operation |
| encoderModel_data_to_embedding | Compute embedding for mini-batch |
| encoderModel_embedding_to_logit | Convert embedding to logit scores |
| encoderModel_gaussian_kernel | Guassian kernel |
| encoderModel_train_encoder | encoder for scAlign |
| encoderModel_train_encoder_multi | encoder for scAlign |
| encoder_small | Network small |
| ExtractGenes | Extracts common set of genes across all datasets |
| gaussianKernel | Computes gaussian kernel matrix |
| GetCharMetadata | Fetch metadata as a character vector |
| GetCrit | Seurat V2 MultiCCA |
| l2n | Seurat V2 MultiCCA |
| MeanDecoderVariance | Calculate mean decoder variance |
| PlotTSNE | Creates tsne plot |
| RunMultiCCA | Seurat V2 MultiCCA |
| scAlign | Run scAlign framework |
| scAlignArguments | Record aguments passed to scAlign |
| scAlignCreateObject | Creates scAlign object |
| scAlignMulti | Run scAlignMultiway alignment |
| scAlignOptions | Set training options |
| SelectColors | Creates a list of unique color values used for plotting |
| UpdateW | Seurat V2 MultiCCA |
