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GRIN2 (version 2.0.0)

Genomic Random Interval (GRIN)

Description

Improved version of 'GRIN' software that streamlines its use in practice to analyze genomic lesion data, accelerate its computing, and expand its analysis capabilities to answer additional scientific questions including a rigorous evaluation of the association of genomic lesions with RNA expression. Pounds, Stan, et al. (2013) .

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Install

install.packages('GRIN2')

Monthly Downloads

144

Version

2.0.0

License

GPL (>= 3)

Issues

0

Pull Requests

0

Stars

1

Forks

0

Maintainer

Abdelrahman Elsayed

Last Published

June 17th, 2025

Functions in GRIN2 (2.0.0)

expr_data

Example T-ALL Gene Expression Dataset
get.chrom.length

Get Chromosome Length
grin.assoc.lsn.outcome

Associate Lesions with Clinical Outcomes
grin.oncoprint.mtx

GRIN OncoPrint-Compatible Lesion Matrix
get.ensembl.annotation

Get Ensembl Gene and Regulatory Features Annotation Data
find.gene.lsn.overlaps

Find Gene Lesion Overlaps
hg38_gene_annotation

Example Gene Annotation Data File
hg38_chrom_size

Chromosome Length Data (hg38)
hg38_cytoband

GRCh38 Chromosome Cytobands
lesion_data

Example T-ALL Lesion Dataset
grin.stats

Execute GRIN Statistical Framework
grin.stats.lsn.plot

GRIN Statistics Lesions Plot
write.grin.xlsx

Write GRIN Results to Excel File
pathways

Genes Annotated to Biological Pathways
prep.binary.lsn.mtx

Prepare Binary Lesion Matrix
lsn.transcripts.plot

Plot of Gene Lesions and Transcripts
prep.lsn.type.matrix

Prepare Lesion Type Matrix
onco.print.props

Oncoprint Proportions by Lesion Type
prep.gene.lsn.data

Prepare Gene and Lesion Data for GRIN Analysis
prob.hits

Find Probability of Locus Hit
top.alex.waterfall.plots

Generate Waterfall Plots for Top Significant Genes
order.index.gene.data

Order and Index Gene Annotation Data
order.index.lsn.data

Order and Index Lesion Data
compute.gw.coordinates

Compute Genome-wide Plotting Coordinates
alex.waterfall.prep

Prepare Lesion and Expression Data for Waterfall Plots
alex.boxplots

Generate Box Plots of Gene Expression by Lesion Groups
KW.hit.express

Associate Lesion Groups with Gene Expression
alex.prep.lsn.expr

Prepare Lesion and Expression Data for Kruskal Wallis Test
count.hits

Count Gene Lesion Hits
default.grin.colors

Assign Default GRIN Colors
alex.waterfall.plot

Generate Waterfall Plot of Lesion and Expression Data
alex.pathway

Visualize Lesion and Expression Data by Pathway
clin_data

Example Clinical Dataset for T-cell Acute Lymphoblastic Leukemia (T-ALL)
grin.barplt

GRIN Lesion Stacked Bar Plot
genomewide.log10q.plot

Genome-wide -log10(q-value) Plot
grin.lsn.boundaries

GRIN Evaluation of Lesion Boundaries
genomewide.lsn.plot

Genome-wide Lesion Plot