Additional analyses¶
Beyond the core edgeR / motif / juDGE pipeline, splicekit ships several further analyses, each runnable as its own splicekit command and included in splicekit process.
Promiscuity: splicekit promisc¶
splicekit promisc
Promiscuity analysis looks at genes and how many of their junctions change across conditions — genes with many independently-regulated junctions ("promiscuous" splicing) versus genes regulated through a single dominant junction.
Cluster of pairwise logFC: splicekit clusterlogfc¶
splicekit clusterlogfc
Clusters comparisons by the logFC of their significant (FDR < 0.05) changes, computed separately at the junction, exon and gene level. This groups comparisons/treatments that produce similar splicing/expression signatures.
JUNE: junction-event analysis¶
splicekit june
JUNE (junction-events) classifies pairs/sets of overlapping junctions into splicing event types — e.g. skipped exons and mutually exclusive exons — by comparing their shared and differing donor/acceptor coordinates, rather than looking at single junctions or exons in isolation.
rMATS¶
splicekit rmats
Runs rMATS on the project's BAM files as an independent, complementary splicing-event caller (skipped exons, alternative 5'/3' splice sites, mutually exclusive exons, retained introns) alongside splicekit's own junction/exon-based analysis.
DEXSeq¶
splicekit dexseq # all feature types
splicekit dexseq junctions # a single feature type
An alternative to splicekit edgeR for differential feature usage, using DEXSeq instead of edgeR. Requires dexseq_scripts to be set in splicekit.config to the path of the DEXSeq R scripts.
DonJuAn: splicekit juan¶
splicekit juan
Merges donor/acceptor anchor edgeR results back into the junction results (results/results_edgeR_junctions.tab), so each junction's row also reports its anchors' differential usage statistics. Runs automatically as part of splicekit process, right after splicekit edgeR.
HTML report: splicekit report¶
splicekit report
Assembles the project's results (edgeR, JUNE, and more) into a browsable HTML report under report/, served together with JBrowse2 when you run splicekit web.