scrapR

Supplementary R package for importing and processing scraps reference and output into R and Seurat. Python-equivalent support is under development.

read reference (if converting to gene-level psi values)

saf <- scrapR::parse_saf_pf("polyadb32.hg38.saf.gz")

read output

mat <- scrapR::scraps_to_matrix("R2_counts.tsv.gz", pf = saf)

insert into Seurat object

so <- scrapR::scraps_to_seurat("R2_counts.tsv.gz", pf = saf, so)

differential usage testing

res <- PA_DEXSeq(mat, cell_ids1, cell_ids2)

report diff RBP motifs from oRNAment annotations

motifs_prep (rna, id1, id2) # by default creates a file hs_motifs_05_oRNAament_rbp.csv.gz
mdb <- read_csv("hs_motifs_05_oRNAament_rbp.csv.gz")
DE_PA_motifs(mdb, res)