Man pages for hiddengenome/altum
deepG
| calculateStepsPerEpoch | Calculate the steps per epoch |
| create_model_lstm_cnn | Creates LSTM/CNN network |
| crispr_full | Example training dataset consiting of a sequence of... |
| crispr_sample | Example training dataset consiting of a sequence of... |
| deepG | deepG for GenomeNet |
| ecoli | E. coli genome for evaluation Can be loaded to workspace via... |
| ecoliCustomScalar | Custom lambda callback that shows accuacy scores for the E.... |
| ecoliEvaluation | Runs a evaluation on the E. coli genome, returns a list of... |
| ecoli_small | subset of the E. coli genome for evaluation Can be loaded to... |
| end_gpu_session | Ends the GPU session |
| evaluateFasta | Evaluates a trained model on .fasta/fastq files |
| extractCellFromStates | Preparing states for tSNE |
| fastaFileGenerator | Custom generator for fasta/fastq files |
| fastaLabelGenerator | Custom generator for fasta files and label targets |
| generateStatesFromFolder | generate states list for tSNE from a fasta folder it is... |
| get_hyper_param | Extract hyperparameters from model |
| getStartInd | Computes start position of samples |
| getStates | Get cell states of semi-redundant chunks |
| getStatesFromFasta | Get cell states from a fasta file |
| getVocabulary | Returns the vocabulary from character string |
| gpuToCpuModel | GPU to CPU model |
| initializeGenerators | Initializes generators defined by labelByFolderGenerator... |
| labelByFolderGenerator | Custom generator for fasta files |
| labelByFolderGeneratorWrapper | Generator wrapper |
| messagef | Wrapper for message(sprintf) |
| nucleotide2value | Change nucleotides to values |
| parenthesis | Training dataset of synthetic parenthesis language Can be... |
| plotTsne | generate and plot tSNE |
| prediction-class | An S4 class for the prediction |
| predictNextNucleotide | Predict next nucleotides in sequence |
| preprocessFasta | Wrapper of the preprocessSemiRedundant()-function |
| preprocessSemiRedundant | Preprocess string to semi-redundant one-hot vector |
| readRowsFromH5 | Read states from h5 |
| replaceChar | Replaces specific nucleotides in a sequence |
| sequenceToArray | One-hot-encodes integer sequence |
| sequenceToArrayLabel | One-hot-encodes integer sequence |
| skip_if_no_keras | Tests if Keras is available for the unit tests |
| startGPUSession | Limit Tensorflow proccess to one or multiple GPUs. |
| statesByFastaOneFile | Write states to h5 file |
| statesWrapper | Inference on set of fasta files |
| trainNetwork | Trains a (mostly) LSTM model on genomic data. Designed for... |
| visualizePrediction | This is a Shiny web application for the visualization of... |
| writeDict | Generates dictionary for LSTMVis |
| writeHdf5 | generates hdf5 file containing the character id for each time... |
| writeStates | Write states to h5 or csv file |
| writeStatesByFastaEntries | Write states to h5 file |
