Man pages for MarianSchoen/DMC
Comparison of different Deconvolution Models in several scenarios
| add_subtype_pheno | add subtype pheno |
| benchmark | main function of the deconvolution benchmark |
| bootstrap_bulks | this functions performs bootstrapping on the real bulk... |
| check_algorithms | check a list of algorithms for compatitbility with benchmark |
| complete_estimates | this function adds rows filled with 0 for all missing cell... |
| create_boxplots | create boxplots of deconvolution results for each algorithm |
| create_bulks | simulate bulk data by summing over single-cell data |
| create_lineplots | create lineplots of deconvolution results and runtime for... |
| create_scatterplots | create scatterplots of deconvolution results for all... |
| create_score_tables | extract matrices of averaged offsets and errors from score... |
| create_sig_matrix | create a signature matrix for usage with CIBERSORT or... |
| deconvolute | deconvolute given bulks with all supplied algorithms and... |
| evaluation_plot | create score plot |
| fine_coarse_subtype_benchmark | fine and coarse subtype benchmark function |
| geneset_benchmark | perform deconvolution of simulated bulks on different gene... |
| get_hclust | Cluster scRNA-Seq data hierarchically, within the input... |
| h5_read_mat | read a simple matrix from hdf5 file |
| h5_write_mat | write a simple matrix to a hdf5 file |
| marker_genes | select marker genes following description in Baron et al.,... |
| plot_all | load results from temp_dir, create all possible plots and... |
| plot_cond_num | create condition number plots for deconvolution results |
| plot_runtime | create barplot of algorithm runtimes |
| prepare_data | convert result lists from benchmark() into data frame for... |
| present_algos | read results written by previous benchmarks and return a list... |
| read_data | read data conforming to the format used by benchmark for data... |
| read_misc_input | read input to benchmark function from hdf5 file |
| read_result_list | read results of deconvolution by different algorithms as... |
| render_results | render markdown report for data produced by benchmark |
| run_deconrnaseq | deconvolute given bulks with DeconRNASeq using single cell... |
| run_dtd | deconvolute given bulk with DTD using single-cell data |
| run_least_squares | deconvolute given bulk with DTD using single-cell data... |
| sample_size_benchmark | training set size benchmark: deconvolute given bulks using... |
| scale_to_count | rescale expression profiles to sum to a fixed count number |
| split_dataset | split dataset in training and test set either by grouping... |
| subtype_plot | create lineplot of algorithm performance across different... |
| write_data | write scRNA-Seq profiles and pheno data, RNA-Seq bulk data... |
| write_misc_input | write some input data of the benchmark to hdf5 |
| write_result_list | write result list as returned by deconvolute and simulation... |
