Man pages for rnabioco/scrapR
scraps output import and processing in R
| as.tbl_intervalcustom | Convert GTF to tibble |
| bin_effectsize | calculation mean diff and effect size of utr3 priming |
| cohens_d | calculation cohens_d effect size |
| countlist_to_bins | calculations from countlist, ready to plot |
| DE_PA_motifs | find motif differences from all differential expression on... |
| dfnot_avg | filter region count list and convert to matrices |
| fill_mat | Fill matrix with 0 rows or columns as needed |
| filter_countlist | filter region count list and convert to matrices |
| knn_smoothing | calculation mean diff and effect size of utr3 priming |
| motifs_prep | prepare motif index from oRNAment files |
| PA_DEXSeq | Run DEXSeq differential expression on polyA sites |
| PA_motifs | find motif differences from 1 pair polyA sites |
| parse_gtf | Parse GTF annotation file |
| parse_saf | Read SAF annotation file |
| parse_saf_pf | Parse SAF annotation file for position factor (pf) values |
| scraps_to_matrix | Read scraps output from umi_tools to sparseMatrix |
| scraps_to_region_counts | Read scraps output to read counts by region type |
| scraps_to_seurat | Add scraps output to existing seurat object as new assay |
