Man pages for VCCRI/Sierra
PolyA counting and differential transcript usage analysis for scRNA-seq data
| AggregatePeakCounts | Aggregate multiple peak count outputs together |
| annotate_gr_from_gtf | Annotates a granges object with overlapping genes from gtf... |
| AnnotatePeaksFromGTF | Annotates a set of peak coordinates from a GTF |
| apply_DEXSeq_test_sce | Apply DEXSeq to detect differential peak usage to a... |
| apply_DEXSeq_test_seurat | Apply DEXSeq to detect differential peak usage |
| BaseComposition | Identify polyA motif and/or polyA stretches from provided... |
| CountPeaks | Generate a peak x cell UMI count matrix |
| DetectAEU | Find alternative 3' end usage between two single-cell... |
| DetectUTRLengthShift | Detect shifts in 3'UTR length usage between cell populations |
| do_arrow_plot | Produce an arrow plot of peak expression |
| DUTest | Apply DEXSeq to detect differential peak usage |
| FindPeaks | Perform splice-aware peak calling on a BAM file produced from... |
| fit_gaussian | Fit Gaussian curve to the coverage |
| gene_Labels | This function has been designed to be called from... |
| generate_merged_peak_table | Merge peaks across data-sets based on a reference |
| generate_self_merged_peaks | Merge a set of peaks |
| generate_self_similarity_table | Generates a table of similarity measures within a set of... |
| generate_similarity_table | Generates a table of similarity measures between two sets of... |
| geneToGR | geneToGR converts a gene symbol to genomic ranges coordinate |
| GetExpressedPeaks | Identify peaks expressed within a certain percentage of cells |
| get_expressed_peaks_sce | Identify highly expressed peaks |
| get_expressed_peaks_seurat | Identify highly expressed peaks |
| GetRelativeExpression | Calculate relative expression between two or more peaks |
| get_relative_expression_sce | Calculate relative expression between two or more peaks |
| get_relative_expression_seurat | Calculate relative expression between two or more peaks |
| make_exons | Helper function |
| make_reference | Build gene start-end reference from a gtf file |
| merge_bam_coverage | merge_bam_coverage |
| MergePeakCoordinates | Merge peaks across a list of data-sets |
| NewPeakSCE | Create a new peak-counts single-cell experiment object from... |
| NewPeakSeurat | Create a new peak-level Seurat object from the peak counts |
| PeakSeuratFromTransfer | Create a peak count Seurat object using a gene-level object |
| PlotCoverage | PlotCoverage |
| PlotRelativeExpressionBox | Generate a box plot plot using relative expression |
| PlotRelativeExpressionTSNE | Generate a t-SNE plot using relative expression |
| PlotRelativeExpressionUMAP | Generate a t-SNE plot using relative expression |
| PlotRelativeExpressionViolin | Generate a violin plot plot using relative expression |
| PlotUTRLengthShift | Plot global shifts in 3'UTR length |
| ReadPeakCounts | Read in peak data saved in MEX format |
| relative_location | Given a peak position in a 3'UTR out of some n number of... |
| rle_to_WIG | load(file="c:/BAM/scRNA_polyA/FC.RData") gtf_file <-... |
| SelectGenePeaks | Return peaks associated with a select gene. |
| SplitBam | Utility to split a bam file into multiple bam files based on... |
