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
example_exon_annotation
                        Example Human Exon Annotation Data
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
                        Retrieve Ensembl Annotation Data
grin.assoc.expr.outcome
                        Association Between Gene Expression and
                        Clinical Outcomes
grin.assoc.lsn.outcome
                        Associate Binary Genomic Lesions with Clinical
                        Outcomes
grin.barplt             GRIN Lesion Stacked Bar Plot
grin.logRank            Log-Rank Test for Associations Between Genomic
                        Lesions and Survival Outcomes
grin.lsn.boundaries     GRIN Evaluation of Lesion Boundaries
grin.oncoprint.mtx      GRIN OncoPrint-Compatible Lesion Matrix
grin.results            Example GRIN2 Analysis Results
grin.stats              Execute the GRIN Statistical Framework
grin.stats.lsn.plot     GRIN Lesion and Statistics Plot
hg38_chrom_size         Chromosome Length Data (GRCh38)
hg38_cytoband           GRCh38 Chromosome Cytobands
hg38_exon_chrom_size    Human GRCh38 Chromosome-Level Exon Target Sizes
hg38_gene_annotation    Example Gene Annotation Data
lesion_data             Example T-ALL Lesion Dataset
lsn.transcripts.plot    Plot Genomic Lesions with Transcript
                        Annotations
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 Significant Genes
write.grin.xlsx         Write GRIN Results to an Excel File
