Man pages for PelzKo/immunedeconv2
Second generation methods for immune cell deconvolution
| anndata_checkload | Checks if anndata package is loaded |
| anndata_is_identical | Check if two anndata objects are identical |
| anndata_to_singlecellexperiment | Convert AnnData to SingleCellExperiment |
| autogenes_checkload | Checks if python and the autogenes module are available and... |
| batch_ids_1 | Patient ids Number 1 from Hao et al. |
| batch_ids_2 | Patient ids Number 2 from Hao et al. |
| batch_ids_3 | Patient ids Number 3 from Hao et al. |
| bseqsc_config | Setup BSeq-SC External Dependencies |
| build_anndata | Create anndata object from single cell expression matrix,... |
| build_model | Building the signature matrix |
| build_model_autogenes | Calculates the signature model with AutoGeneS. This function... |
| build_model_bayesprism | No model is built as BayesPrism performs signature building... |
| build_model_bisque | No model is build as Bisque does both steps in one. |
| build_model_bseqsc | Calculates the signature model with BSeq-sc |
| build_model_cdseq | No model is build as CDSeq does both steps in one. |
| build_model_cibersortx | Signature matrix creation with CIBERSORTx |
| build_model_cpm | No model is build as CPM does not use a signature matrix. |
| build_model_dwls | Signature matrix creation with DWLS using genes identified by... |
| build_model_momf | Calculates the signature model with MOMF |
| build_model_music | Signature creation with MuSiC. |
| build_model_scaden | Builds Scaden Model from scRNA data |
| build_model_scdc | Signature creation with SCDC. |
| bulk | Example RNA-seq dataset from Hoek et al. |
| calc_condition_number | Calculation of the condition number |
| calculate_cell_embedding | Calculation of the cell_space parameter needed by CPM |
| cell_type_annotations_1 | Cell Type Annotations Number 1 from Hao et al. |
| cell_type_annotations_2 | Cell Type Annotations Number 2 from Hao et al. |
| cell_type_annotations_3 | Cell Type Annotations Number 3 from Hao et al. |
| check_and_install | Checking and installing all dependencies for the specific... |
| check_container | Checks wether docker/apptainer are available and can be used |
| check_credentials | Checks that the email and token variables are set |
| convert_to_matrix | Converts the object into a matrix |
| create_container_command | Creation of the docker command |
| deconvolute | Deconvolution |
| deconvolute_autogenes | Deconvolution Analysis using AutoGeneS. One-step function... |
| deconvolute_bayesprism | Bayesian deconvolution module using BayesPrism |
| deconvolute_bisque | Calculates the decomposition using the bisque algorithm... |
| deconvolute_bseqsc | Deconvolution Analysis using BSeq-sc |
| deconvolute_cdseq | CDSeq Deconvolution |
| deconvolute_cibersortx | Deconvolute with CIBERSORTx |
| deconvolute_cpm | CPM Deconvolution |
| deconvolute_dwls | Calculates the decomposition using the dwls algorithm |
| deconvolute_momf | Deconvolution Analysis using MOMF (via Nonnegative... |
| deconvolute_music | MuSiC Deconvolution |
| deconvolute_scaden | Performs deconvolution with Scaden |
| deconvolute_scdc | SCDC Deconvolution |
| deconvolution_methods | List of supported deconvolution methods |
| deescape_special_chars | Removes the substitutions and turns them back into the... |
| dot-bisque_patched_deconvolution | Calculates the decomposition using the bisque algorithm |
| dot-bisque_patched_model | Calculates the signature model with bisque |
| escape_special_chars | Removes special characters by substituting them with unique... |
| extract_signature_autogenes | Extraction of the signature matrix from autogenes .pickle... |
| get_cell_fractions_options | Creation of the options of the "get cell fractions" docker... |
| get_method_options | Creation of the additional parameter sting for the docker... |
| get_signature_matrix_options | Creation of the options of the "get signature matrix" docker... |
| get_single_cell_expression_set | Generating a single cell expression set |
| init_python | Initiates python environment |
| install_all_python | Install all python packages |
| install_autogenes | Install AutoGeneS |
| install_scaden | Install Scaden |
| make_barplot | Plot deconvolution results as a barplot |
| make_benchmarking_scatterplot | Make a Scatterplot for Benchmarking |
| matrix_to_singlecellexperiment | Convert count matrix to SingleCellExperiment |
| normalize_deconv_results | Normalize deconvolution result |
| omnideconvstartup | Manage python dependencies according to:... |
| plot_deconvolution | Plot Deconvolution results |
| python_available | Checks if python is available in environment |
| read_anndata | Read anndata object (.h5ad format) |
| RefData | Gold standard measurements with FACS from Hoek et al. |
| required_packages | The dependencies for each method |
| save_as_h5ad | Save as .h5ad |
| scaden_checkload | Checks if scaden is installed. |
| scaden_predict | Predict cell proportions |
| scaden_process | Pre-processes training data |
| scaden_simulate | Simulates training data from scRNA data |
| scaden_simulate_example | Simulates example Data provided by Scaden |
| scaden_train | Trains a Scaden model |
| sces_are_identical | Check if two SingleCellExperiments are identical |
| set_cibersortx_credentials | Setting the CIBERSORTx Credentials |
| set_python | Defines python path. |
| setup_apptainer_container | Setup of the apptainer container |
| single_cell_data_1 | Example single-cell RNA-seq dataset Number 1 from Hao et al. |
| single_cell_data_2 | Example single-cell RNA-seq dataset Number 2 from Hao et al. |
| single_cell_data_3 | Example single-cell RNA-seq dataset Number 3 from Hao et al. |
| singlecellexperiment_to_anndata | Convert SingleCellExperiment to AnnData object |
| singlecellexperiment_to_matrix | Convert SingleCellExperiment to Matrix + annotation vector... |
| transform_and_save_bulk | Creation of the bulk data file in the CIBERSORTx required... |
| transform_and_save_single_cell | Creation of the single cell data file in the CIBERSORTx... |
| verbose_wrapper | A wrapper function whether to suppress messages |
| write_anndata | Write anndata object (.h5ad format) |
