Man pages for lulizou/spASE
Detecting Allele-Specific Expression in Spatial Transcriptomics
| aggregate_cell_types | Aggregates the pixel occurrences for each cell type in the... |
| betabinase | Helper function to fit betabin model while handling common... |
| build.designmatrix.intercept | Constructs a design matrix for running CSIDE with only an... |
| build.designmatrix.nonparam | Constructs a design matrix for running CSIDE... |
| build.designmatrix.regions | Constructs a design matrix for running CSIDE across a set of... |
| build.designmatrix.single | Constructs a design matrix for running CSIDE with a single... |
| choose_sigma_c | Estimates sigma_c by maximum likelihood |
| convert.old.RCTD | Updates an old 'RCTD' object to be compatible with the... |
| count_cell_types | Counts number of pixel occurrences for each cell type to be... |
| create.RCTD | Creates an 'RCTD' object from a scRNA-seq reference... |
| create_RCTD_plots | Create all plots for an RCTD object after cell types have... |
| create.RCTD.replicates | Creates an 'RCTD.replicates' object across multiple... |
| CSIDE.population.inference | Runs population-level differential expression inference for a... |
| cside_spase | Main function for detecting spatial allele-specific... |
| expit | expit function |
| exvar.celltocell.interactions | Constructs an explanatory variable representing density of a... |
| exvar.point.density | Constructs an explanatory variable representing density of a... |
| fitBulk | Performs Platform Effect Normalization: |
| fitPixels | Runs the RCTD algorithm |
| get_cell_type_info | Computes cell type profiles in a scRNA-seq dataset |
| get_decomposed_data | Decomposes SpatialRNA data into individual cells |
| get_de_genes | Returns a list of differentially expressed genes |
| get_doublet_weights | Converts RCTD doublet mode results to a weight matrix (across... |
| get_norm_ref | Normalizes cell type profiles to a target dataset |
| getSplineMatrix | Helper function to get normalized spline basis function... |
| get_standard_errors | On an RCTD object after running CSIDE, returns an array of... |
| import_weights | Assigns a cell type 'weights' matrix to an 'RCTD' object |
| make_all_de_plots | Makes all CSIDE plots on RCTD object, after running CSIDE |
| make_de_plots_genes | Makes spatial gene CSIDE plots (colored continuously) on RCTD... |
| make_de_plots_quant | Makes quantitative CSIDE plots on RCTD object, after running... |
| make_de_plots_regions | Makes spatial gene CSIDE plots (colored by discrete regions)... |
| make_de_plots_replicates | Makes spatial gene CSIDE plots (colored by two discrete... |
| make_de_plots_spatial | Makes spatial gene CSIDE plots (colored by two discrete... |
| merge.RCTD.objects | Creates an 'RCTD.replicates' object across multiple 'RCTD'... |
| normalize_weights | Normalizes the 'weights' matrix from the RCTD results object |
| plot_all_cell_types | Plots all cell types in space |
| plot_class | Plots a factor variable in space on the puck |
| plot_cond_occur | Barplot of the confident counts for each cell type |
| plot_doublets | Plots all doublets in space |
| plot_doublets_type | Plots doublets of each cell type individually |
| plot_doub_occur_stack | Plots doublet co-occurances |
| plot_gene_raw | Makes a spatial plot of continuous gene expression for a... |
| plot_gene_regions | Makes a spatial plot of gene expression for a particular gene... |
| plot_gene_two_regions | Makes a spatial plot of gene expression for a particular gene... |
| plot_occur_unthreshold | Barplot of the counts for each cell type |
| plot_prediction_gene | Makes a spatial plot of CSIDE fitted gene expression |
| plot_puck_continuous | Plots a continuous value over locations on the puck |
| plot_puck_wrapper | Plots a continuous value over filtered locations on the puck |
| plotScase | Main function for plotting ASE fits in single-cell data |
| plotSpase | Main function for plotting ASE fits from spase fit |
| plot_weights | Spatially plot the confident weights for each cell type |
| plot_weights_doublet | Spatially plot the weights for each cell type in doublet_mode |
| plot_weights_unthreshold | Spatially plot all weights for each cell type |
| process_beads_batch | Runs RCTD in doublet mode on 'puck' |
| process_data | Runs RCTD in full mode on 'puck' |
| quasibinase | Helper function to fit quasibinomial model while handling... |
| RCTD-class | An S4 class used to run the RCTD and CSIDE algorithms |
| RCTD.replicates-class | An S4 class used to store multiple replicates as 'SpatialRNA'... |
| read.SpatialRNA | Creates a SpatialRNA object from a coords and counts file |
| read.VisiumSpatialRNA | Creates a SpatialRNA object from a 10x Genomics Visium 'outs'... |
| Reference | constructor of 'Reference' object |
| Reference-class | An S4 class to represent Single-Cell RNA-seq reference |
| restrict_counts | Restricts a SpatialRNA object to a subset of genes (and... |
| restrict_puck | Restricts a SpatialRNA object to a subset of pixels |
| run.CSIDE | Runs cell type specific CSIDE on a 'RCTD' object with a... |
| run.CSIDE.general | Runs CSIDE on a 'RCTD' object with a general design matrix |
| run.CSIDE.intercept | Runs CSIDE in intercept-only mode |
| run.CSIDE.nonparam | Runs CSIDE on a 'RCTD' object to detect nonparametric smooth... |
| run.CSIDE.regions | Runs CSIDE on a 'RCTD' object for DE across multiple discrete... |
| run.CSIDE.replicates | Runs CSIDE on a 'RCTD.replicates' object |
| run.CSIDE.single | Runs CSIDE on a 'RCTD' object with a single explanatory... |
| run.RCTD | Runs the RCTD pipeline on a 'RCTD' object |
| run.RCTD.replicates | Runs the RCTD pipeline on a 'RCTD.replicates' object |
| save.CSIDE.replicates | Saves the CSIDE population-level differential expression... |
| scase | Main function for estimating ASE in single-cell data |
| set_cell_types_assigned | If cell types have been assigned to the RCTD object, running... |
| set_likelihood_vars | Sets Precomputed Probabiliites as Global Variable |
| spacexr | spacexr: an R package for assigning cell types and cell type... |
| spase | Main function for detecting spatial allele-specific... |
| SpatialRNA | constructor of SpatialRNA object |
| SpatialRNA-class | An S4 class to represent Spatial Transcriptomic data |
| write_de_summary | Saves to csv the CSIDE significant gene dataframes after... |
