Package index • splikit

R6 Object Interface

Modern object-oriented interface for splicing analysis

SplikitObject: SplikitObject

Main Functions

Core functions for splicing analysis

make_m1(): make_m1
make_m2(): make_m2 (Integrated with Automatic Batching)
make_junction_ab(): make_junction_ab
make_gene_count(): make_gene_count
make_velo_count(): Process Spliced and Unspliced Counts from Velocyto Outputs
make_eventdata_plus(): make_eventdata_plus

Visualisation

Splice-junction and gene-model plots

plot_exclusive_junctions(): Plot transcript-exclusive splice junctions
plot_exclusive_junctions_event(): Plot transcript-exclusive splice junctions observed in eventdata
plot_exclusive_junctions_pdf(): Multi-page PDF of transcript-exclusive junctions
print(<splikit_junction_plot>): Print method for splikit junction-plot results

Feature Selection

Functions for identifying variable splicing events

find_variable_genes(): Find Variable Genes Using Variance or Deviance-Based Metrics
find_variable_events(): Calculate the Sum Deviance for Inclusion and Exclusion Matrices
get_rowVar(): Calculate Row-wise Variance for Dense or Sparse Matrices

Analysis Functions

Additional analysis utilities

get_pseudo_correlation(): Compute Pseudo-Correlation Using Beta-Binomial Model
get_silhouette_mean(): Compute Average Silhouette Width with Logging

Data

Example datasets

load_toy_M1_M2_object(): Load the toy M1/M2 object
load_toy_SJ_object(): Load the toy SJ object

Package

Package information

splikit(): Create a SplikitObject