Man pages for AllenInstitute/L5_VEN
| annotate_cat | Generate colors and ids for categorical annotations. From... |
| annotate_factor | Generate colors and ids for categorical annotations that are... |
| annotate_num | Generate colors and ids for numeric annotations. From... |
| auto_annotate | Automatically format an annotation file. From... |
| build_header_labels | Build colorful, rectangular labels for plot headers in plot... |
| build_layer_plot | Function to build the jittered layer plot + dendrogram. From... |
| build_legend_plot | This function builds a legend plot. THIS FUNCTION IS NOW IN... |
| calc_beta | Calculates the beta score |
| clusterInfoMTG | Cluster information for MTG data set. |
| compareClusterCalls | Compare two cluster sets matched to CCA. From... |
| error.bar | Adds an error bar |
| errorBarPlot | Plots and error bar |
| ExtractField | (From Seurat) Extract delimiter information from a string. |
| FI_layer5_count_data | snRNA-seq data from frontoinsula |
| FI_layer5_sample_information | Sample information for nuclei from frontoinsula. |
| findFromGroups | Feturns the summary gene expression value across a group |
| FindNeighbors | (From Seurat) FindNeighbors (required for Windows... |
| formatPlotGenes | Function for getting the plotting genes (to avoid typing it... |
| getAnovaPvalforApply | ANOVA for use with the apply function |
| getBetaScore | Wrapper for calc_beta |
| getDend | Builds a clustering tree |
| get_feather_data | Read data from a directory of feather files. From... |
| get_node_dend | Function to subset a dendrogram by retrieving a node with a... |
| getTopMarkersByProp | Function for getting top marker genes |
| getTopMarkersByProp2 | Function for getting top marker genes |
| getTopMarkersByPropNew | Function for getting top marker genes |
| group_annotations | Group annotation columns. From library(scrattch.io) |
| group_heatmap_plot | Heatmap plots of group summary statistics. THIS FUNCTION IS... |
| group_violin_plot | Violin plots of gene expression for clusters |
| hello | Hello, World! |
| labelDend | Labels a clustering tree |
| LogSeuratCommand | (From Seurat) logs a command |
| meanEx | Mean expression |
| mito_genes | Mitochondrial-associated genes. |
| mixColors | Returns the average color from a vector of colors |
| mouse2human2 | Conversion between mouse and human gene names (not used) |
| plot_dend | Allows plot_dend to work properly in a for loop. |
| plot_dend2 | Plots the dendrogram in a convenient format. From library... |
| pt2mm | Convert font sizes in pt to mm |
| qcPlot | Makes QC plots. From library(patchseqtools) |
| rankCompleteDendPlot | Wrapper for plot_dend |
| renameClusters | Another function for renaming clusters based on data and... |
| reorder.dend | Reorders a clustering tree. Function from... |
| reorder_matrix | Reorder a matrix. From library(patchseqtools) |
| rowMax | Return the row max |
| sample_heatmap_plot | Heatmaps of gene expression for individual samples. THIS... |
| sci_label | Convert integers to scientific notation labels |
| sex_genes | Sex-associated genes. |
| subsampleCells | Subsample cells. THIS FUNCTION IS IN library(mfishtools) |
| summarySE | Get some summary statistics. From library(patchseqtools) |
| t.test.l | t.test wrapper for use with the "apply" function |
| t.test.l.paired | Paired t.test wrapper for use with the "apply" function |
| updateAndOrderClusters | Function for updating and ordering clusters based on... |
| updateSampDat | Update the sample data |
| values_to_colors | Convert values to colors along a color ramp. From... |
| varibow | Generate a rainbow palette with variation in saturation and... |
