KW.hit.express          Associate Lesion Groups with Gene Expression
alex.boxplots           Generate Box Plots of Gene Expression by Lesion
                        Groups
alex.pathway            Visualize Lesion and Expression Data by Pathway
alex.prep.lsn.expr      Prepare Lesion and Expression Data for Kruskal
                        Wallis Test
alex.waterfall.plot     Generate Waterfall Plot of Lesion and
                        Expression Data
alex.waterfall.prep     Prepare Lesion and Expression Data for
                        Waterfall Plots
clin_data               Example Clinical Dataset for T-cell Acute
                        Lymphoblastic Leukemia (T-ALL)
compute.gw.coordinates
                        Compute Genome-wide Plotting Coordinates
count.hits              Count Gene Lesion Hits
default.grin.colors     Assign Default GRIN Colors
expr_data               Example T-ALL Gene Expression Dataset
find.gene.lsn.overlaps
                        Find Gene Lesion Overlaps
genomewide.log10q.plot
                        Genome-wide -log10(q-value) Plot
genomewide.lsn.plot     Genome-wide Lesion Plot
get.chrom.length        Get Chromosome Length
get.ensembl.annotation
                        Get Ensembl Gene and Regulatory Features
                        Annotation Data
grin.assoc.lsn.outcome
                        Associate Lesions with Clinical Outcomes
grin.barplt             GRIN Lesion Stacked Bar Plot
grin.lsn.boundaries     GRIN Evaluation of Lesion Boundaries
grin.oncoprint.mtx      GRIN OncoPrint-Compatible Lesion Matrix
grin.stats              Execute GRIN Statistical Framework
grin.stats.lsn.plot     GRIN Statistics Lesions Plot
hg38_chrom_size         Chromosome Length Data (hg38)
hg38_cytoband           GRCh38 Chromosome Cytobands
hg38_gene_annotation    Example Gene Annotation Data File
lesion_data             Example T-ALL Lesion Dataset
lsn.transcripts.plot    Plot of Gene Lesions and Transcripts
onco.print.props        Oncoprint Proportions by Lesion Type
order.index.gene.data   Order and Index Gene Annotation Data
order.index.lsn.data    Order and Index Lesion Data
pathways                Genes Annotated to Biological Pathways
prep.binary.lsn.mtx     Prepare Binary Lesion Matrix
prep.gene.lsn.data      Prepare Gene and Lesion Data for GRIN Analysis
prep.lsn.type.matrix    Prepare Lesion Type Matrix
prob.hits               Find Probability of Locus Hit
top.alex.waterfall.plots
                        Generate Waterfall Plots for Top Significant
                        Genes
write.grin.xlsx         Write GRIN Results to Excel File
