Pathway analysis of alternative splicing would be biased without accounting for the different number of exons or junctions associated with each gene, because genes with higher number of exons or junctions are more likely to be included in the significant gene list in alternative splicing. We present PathwaySplice, an R package that (i) Performs pathway analysis that explicitly adjusts for the number of exons or junctions associated with each gene, (ii) visualizes selection bias due to different number of exons or junctions for each gene and formally tests for presence of bias using logistic regression, (iii) supports gene sets based on the Gene Ontology terms, as well as more broadly defined gene sets (e.g. MSigDB) or user defined gene sets, (iv) identifies the significant genes driving pathway significance and (v) organizes significant pathways with an enrichment map, where pathways with large number of overlapping genes are grouped together in a network graph.