The plots are generated using ggplot2.
The Percent Spliced In (PSI) value is a common, intuitive ratio for quantifying splicing events (1).

Motivation Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. psiplot psiplot is an R package for generating plots of percent spliced-in (PSI) values of alternatively-spliced exons that were computed by vast-tools, an RNA-Seq pipeline for alternative splicing analysis.


For each sample and every possible splice event (e.g. an exon skip event), we calculate a percent-splice-in (PSI) value. Investigators can interrogate genes of interest, search for the genes that show the strongest variation between or among selected tumor types, or explore splicing pattern changes between tumor and adjacent normal … PSI is the ratio of normalized read counts indicating inclusion of a transcript element over the total normalized reads for that event (both inclusion and exclusion reads).

The PSI is therefore 8/10 or 0.8 indicating that 80% of the transcripts in the sample include exon 3. psi: Calculate percent spliced-in (Psi/Ψ) scores for your data from the splicing events you created¶ Overview ¶ outrigger psi uses the splicing events created by outrigger index , or, if outrigger validate has been run, only the valid alternative splicing events with appropriate splice sites.

Percent Spliced In (PSI) values for splice events on samples from 33 different tumor types, including available adjacent normal samples, have been loaded into TCGA SpliceSeq. the definition given in their paper is: 'percentage spliced in' (PSI or Ψ)11denotes the fraction of mRNAs that represent the inclusion isoform. The PSI value of exonic part 4 indicates the efficiency of the 3 acceptor site of the second intron. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data.

Splicing events in each subtype were regarded as signatures if their mean PSI values were 30% higher than those in any other subtype (FDR < 0.05). Statistical analysis was performed by using the Mann-Whitney U test. (D) SpliceSeq evaluates all of the listed types of splice events.


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